Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

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metaboigniter
metaboigniter
metaboigniter
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Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data .

Introduction

nf-core/metaboigniter is bioinformatics pipeline for pre-processing of mass spectrometry-based metabolomics data.

The workflow performs MS1 based quantification and MS2 based identification using combination of different modules. The following steps can be performed using the workflow:

nf-core/metaboigniter-workflow

  • Centroiding (optional): Also referred to as peak pickering is a step that reduce the distribution of ions derived from a single mass to the peak of the distribution.

  • parameter tuning using IPO: MS1 quantification and library characterization parameters can be tuned using IPO

  • mass trace detection: The ions derived from the same analytes are clustered together forming a mass trace. These are the entities that will be used for quantification.

  • mass trace matching and retention time (RT) correction: The mass traces across different samples will be match against each other and RT shift between the samples will be adjusted.

  • filtering (optional): The mass traces will be filtered out based on the QC samples.

  • Annotation: The isotopes and adducts will be annotated in this step.

  • MS2 (identification): At the moment we support two types of identification: in-silico and identificaiton based on internal library. This will be expanded in the corresponding section. At the moment we do not support MS1-based identification.

The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

  1. Install nextflow ( >=20.04.0 )

  2. Install any of Docker , Singularity , Podman , Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs )

  3. Download the pipeline and test it on a minimal dataset with a single command 

    nextflow run nf-core/metaboigniter -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>

    Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

  4. Start running your own analysis!

    We highly recommend that you follow our usage documentation . Since the number of parameters is large, it's going to be a fairly complex bash command to run the workflow. Nevertheless, the parameters can always be passed to the workflow as argument using two dashes "--".

    See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/metaboigniter pipeline comes with documentation about the pipeline: usage and output .

Credits

nf-core/metaboigniter was originally written by Payam Emami.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines .

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite ).

Citation

If you use nf-core/metaboigniter for your analysis, please cite it using the following doi: 10.5281/zenodo.4743790

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x .

In addition, references of tools and data used in this pipeline are as follows:

  1. Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S: CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem 84:283-289.

  2. Benton HP, Wong DM, Trauger SA, Siuzdak G: XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization. Anal Chem 80(16):6382-6389. doi:10.1021/ac800795f.

  3. Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics. 2008;9:163. doi:10.1186/1471-2105-9-163.

  4. Libiseller G, Dvorzak M, Kleb U, Gander E, Eisenberg T, Madeo F, Neumann S, Trausinger G, Sinner F, Pieber T, Magnes C ((2015)). “IPO: a tool for automated optimization of XCMS parameters.” BMC Bioinformatics, 16, 118.

  5. Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, and Sebastian Böcker. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A, 112(41):12580-12585, 2015. (cite this when using CSI:FingerID)

  6. Ruttkies C., Schymanski E.L. et al, MetFrag relaunched: incorporating strategies beyond in silico fragmentation. Journal of Cheminformatics, 2016, 8:3.

  7. Allen F, Greiner R, and Wishart D. Computational prediction of electron ionization mass spectra to assist in GC-MS compound identification. Submitted, 2016.

  8. Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Felix Nothias, Kai Dührkop, Nuno Bandeira, Pieter C Dorrestein, Sebastian Böcker. Significance estimation enabling large scale untargeted metabolomics annotations. Nature Communications, 2017. 8(1494)

Third party software copyright

nf-core/metaboigniter contains several scripts for performing various pre-processing steps.

The following software have not been written by us:

  • MetFrag (GNU LGPL v2.1 or later). Files included:

    • bin/metfrag

    • bin/metfrag.jar

  • jni-inchi (GNU LGPL v3). Files include:

    • bin/jni-inchi-0.8.jar

The rest of the scripts has been originally written by Payam Emami as part of PhenoMeNal (Phenome and Metabolome aNalysis) consortium .

Code Snippets

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"""

echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
Rscript -e "cat(as.character(packageVersion('CAMERA')),'\\n')" &> v_camera.txt
Rscript -e "cat(as.character(packageVersion('xcms')),'\\n')" &> v_xcms.txt
Rscript -e "cat(as.character(packageVersion('MSnbase')),'\\n')" &> v_msnbase.txt
Rscript -e "cat(as.character(packageVersion('IPO')),'\\n')" &> v_ipo.txt
OpenMSInfo |  grep -oP -m 1 '([0-9][.][0-9][.][0-9])' &> v_openms.txt
sh /usr/bin/CSI/bin/sirius.sh --loglevel=OFF --version 2>1 | grep -oP -m 1 '([0-9][.][0-9][.][0-9])' &> v_sirius.txt

scrape_software_versions.py &> software_versions_mqc.yaml
"""
NextFlow From line 423 of 1.0.1/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 463 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 492 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 516 of 1.0.1/main.nf 
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"""
touch quant_params_pos.json
touch rt_params_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_pos_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_pos \\
    columnToSelect=$params.ipo_columnToSelect_pos  \\
    valueToSelect=$params.ipo_valueToSelect_pos \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ncores=$params.ipo_ncores_pos \\
    outputxset=quant_params_pos.json \\
    outputrt=rt_params_pos.json
"""
NextFlow IPO From line 554 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_pos_xcms \\
    noise=$params.noise_quant_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    mzdiff=$params.mzdiff_quant_pos_xcms \\
    snthresh=$params.snthresh_quant_pos_xcms  \\
    prefilter_l=$params.prefilter_quant_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_pos_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_pos_xcms \\
    integrate=$params.integrate_quant_pos_xcms  \\
    fitgauss=$params.fitgauss_quant_pos_xcms \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos  \\
    mzCenterFun=$params.ipo_mzCenterFun_pos \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    ipo_inv=$ipo_pos_localQ \\
    $filter_argument
"""
NextFlow From line 639 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 710 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos  \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 733 of 1.0.1/main.nf 
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"""
touch quant_params_pos.json
touch rt_params_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_pos_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_pos \\
    columnToSelect=$params.ipo_columnToSelect_pos  \\
    valueToSelect=$params.ipo_valueToSelect_pos \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ncores=$params.ipo_ncores_pos \\
    outputxset=quant_params_pos.json \\
    outputrt=rt_params_pos.json
"""
NextFlow IPO From line 769 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_pos_xcms \\
    peakwidthHigh=$params.peakwidthhigh_quant_pos_xcms  \\
    noise=$params.noise_quant_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos  \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    mzdiff=$params.mzdiff_quant_pos_xcms \\
    snthresh=$params.snthresh_quant_pos_xcms \\
    prefilter_l=$params.prefilter_quant_pos_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_pos_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_pos_xcms \\
    integrate=$params.integrate_quant_pos_xcms  \\
    fitgauss=$params.fitgauss_quant_pos_xcms \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    ipo_inv=$ipo_pos_localQ \\
    $filter_argument
"""
NextFlow From line 854 of 1.0.1/main.nf 
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"""
nextFlowDIR=\$PWD
xcmsCollect.r input=$inputs_aggregated output=collection_pos.rdata
"""
NextFlow From line 921 of 1.0.1/main.nf 
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"""
retCor.r \\
    input=\$PWD/$rdata_files \\
    output=RTcorrected_pos.rdata \\
    method=obiwarp \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos  \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ipo_inv=$ipo_pos_localRT \\
    ncores=$params.ipo_ncores_pos  \\
    profStep=$params.profStep_align_N1_pos_xcms \\
    center=$params.center_align_N1_pos_xcms \\
    response=$params.response_align_N1_pos_xcms  \\
    distFunc=$params.distFunc_align_N1_pos_xcms \\
    gapInit=$params.gapInit_align_N1_pos_xcms \\
    gapExtend=$params.gapExtend_align_N1_pos_xcms  \\
    factorDiag=$params.factorDiag_align_N1_pos_xcms \\
    factorGap=$params.factorGap_align_N1_pos_xcms \\
    localAlignment=$params.localAlignment_align_N1_pos_xcms \\
    $filter_argument \\
    inputraw=$inputs_aggregated
"""
NextFlow From line 948 of 1.0.1/main.nf 
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"""
group.r \\
    input=$rdata_files \\
    output=groupN1_pos.rdata \\
    bandwidth=$params.bandwidth_group_N1_pos_xcms \\
    minfrac=$params.minfrac_group_N1_pos_xcms \\
    minsamp=$params.minsamp_group_N1_pos_xcms \\
    max=$params.max_group_N1_pos_xcms  \\
    mzwid=$params.mzwid_group_N1_pos_xcms
"""
NextFlow From line 1010 of 1.0.1/main.nf 
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"""
blankfilter.r \\
    input=$rdata_files \\
    output=blankFiltered_pos.rdata \\
    method=$params.method_blankfilter_pos_xcms \\
    blank=$params.blank_blankfilter_pos_xcms \\
    sample=$params.sample_blankfilter_pos_xcms \\
    rest=$params.rest_blankfilter_pos_xcms
"""
NextFlow From line 1042 of 1.0.1/main.nf 
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"""
dilutionfilter.r \\
    input=$rdata_files \\
    output=dilutionFiltered_pos.rdata \\
    Corto=$params.corto_dilutionfilter_pos_xcms  \\
    dilution=$params.dilution_dilutionfilter_pos_xcms \\
    pvalue=$params.pvalue_dilutionfilter_pos_xcms \\
    corcut=$params.corcut_dilutionfilter_pos_xcms \\
    abs=$params.abs_dilutionfilter_pos_xcms
"""
NextFlow From line 1074 of 1.0.1/main.nf 
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"""
cvfilter.r \\
    input=$rdata_files \\
    output=cvFiltered_pos.rdata \\
    qc=$params.qc_cvfilter_pos_xcms \\
    cvcut=$params.cvcut_cvfilter_pos_xcms
"""
NextFlow From line 1108 of 1.0.1/main.nf 
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"""
xsAnnotate.r  input=$rdata_files output=CameraAnnotatePeaks_pos.rdata
"""
NextFlow From line 1137 of 1.0.1/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=CameraGroup_pos.rdata \\
    sigma=$params.sigma_group_pos_camera \\
    perfwhm=$params.perfwhm_group_pos_camera \\
    intval=$params.intval_group_pos_camera
"""
NextFlow From line 1158 of 1.0.1/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=CameraFindAdducts_pos.rdata \\
    ppm=$params.ppm_findaddcuts_pos_camera \\
    polarity=$params.polarity_findaddcuts_pos_camera
"""
NextFlow From line 1185 of 1.0.1/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=CameraFindIsotopes_pos.rdata \\
    maxcharge=$params.maxcharge_findisotopes_pos_camera
"""
NextFlow From line 1210 of 1.0.1/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 1241 of 1.0.1/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$input_args \\
    output=MapMsms2Camera_pos.rdata \\
    ppm=$params.ppm_mapmsmstocamera_pos_msnbase \\
    rt=$params.rt_mapmsmstocamera_pos_msnbase
"""
NextFlow From line 1268 of 1.0.1/main.nf 
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"""
mkdir out

MS2ToMetFrag.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=out  \\
    precursorppm=$params.precursorppm_msmstoparam_pos_msnbase \\
    fragmentppm=$params.fragmentppm_msmstoparam_pos_msnbase \\
    fragmentabs=$params.fragmentabs_msmstoparam_pos_msnbase  \\
    database=$params.database_msmstoparam_pos_msnbase \\
    mode=$params.mode_msmstoparam_pos_msnbase \\
    adductRules=$params.adductRules_msmstoparam_pos_msnbase \\
    minPeaks=$params.minPeaks_msmstoparam_pos_msnbase

ls out/ -A -1  | cut -d'_' -f4- | tr ' ' '\n' | sort -u | xargs -I %  find out/ -type f -iname *% -exec zip %.zip {} +
"""
NextFlow From line 1296 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}_class_Csifingerid_pos.csv

fingerID.r \\
    input=\$PWD/inputs \\
    database=$params.database_csifingerid_pos_csifingerid \\
    tryOffline=T  \\
    output=\$PWD/outputs/ \\
    ncores=$params.ncore_csifingerid_pos_csifingerid \\
    timeout=$params.timeout_csifingerid_pos_csifingerid \\
    canopus=T \\
    canopusOutput=\$PWD/${parameters.baseName}_class_Csifingerid_pos.csv

zip -j -r ${parameters.baseName}_Csifingerid_pos.zip outputs/*.csv
"""
NextFlow From line 1341 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r Csifingerid_pos.zip all

aggregateMetfrag.r \\
    inputs=Csifingerid_pos.zip \\
    realNames=Csifingerid_pos.zip \\
    output=aggregated_identification_csifingerid_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_csifingerid_pos.csv
"""
NextFlow From line 1377 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_csifingerid_pos.csv \\
        readTable=T
else
    touch pep_identification_csifingerid_pos.csv
fi
"""
NextFlow From line 1410 of 1.0.1/main.nf 
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"""
if [ -s $csifingerid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$csifingerid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_csifingerid.txt \\
        outputVariables=varsPOSout_pos_csifingerid.txt \\
        outputMetaData=metadataPOSout_pos_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_csifingerid.txt  \\
        outputVariables=varsPOSout_pos_csifingerid.txt \\
        outputMetaData=metadataPOSout_pos_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1440 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_pos_metfrag \\
        run_metfrag.sh \\
        -p {} \\
        -f \$PWD/outputs/{/.}.csv \\
        -l "\$PWD/$metfrag_database" \\
        -s "OfflineMetFusionScore"
zip -j -r ${parameters.baseName}_metfrag_pos.zip outputs/*.csv
"""
NextFlow From line 1536 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r metfrag_pos.zip all

aggregateMetfrag.r \\
    inputs=metfrag_pos.zip \\
    realNames=metfrag_pos.zip \\
    output=aggregated_identification_metfrag_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_metfrag_pos.csv
"""
NextFlow From line 1569 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ];then
    metfragPEP.r \\
        input=$identification_result \\
        score=FragmenterScore \\
        output=pep_identification_metfrag_pos.csv \\
        readTable=T
else
    touch pep_identification_metfrag_pos.csv
fi
"""
NextFlow From line 1601 of 1.0.1/main.nf 
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"""
if [ -s $metfrag_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$metfrag_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
        combineReplicate=$params.combine_replicate_output_pos_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_metfrag.txt \\
        outputVariables=varsPOSout_pos_metfrag.txt \\
        outputMetaData=metadataPOSout_pos_metfrag.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore  \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera  \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_metfrag.txt \\
        outputVariables=varsPOSout_pos_metfrag.txt \\
        outputMetaData=metadataPOSout_pos_metfrag.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1633 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_pos_cfmid cfmid.r \\
        input={} \\
        realName={/} \\
        databaseFile=\$PWD/$cfmid_database  \\
        output=\$PWD/outputs/{/.}.csv \\
        candidate_id=$params.candidate_id_identification_pos_cfmid \\
        candidate_inchi_smiles=$params.candidate_inchi_smiles_identification_pos_cfmid \\
        candidate_mass=$params.candidate_mass_identification_pos_cfmid \\
        databaseNameColumn=$params.database_name_column_identification_pos_cfmid \\
        databaseInChIColumn=$params.database_inchI_column_identification_pos_cfmid \\
        scoreType=Jaccard

zip -j -r ${parameters.baseName}_cfmid_pos.zip outputs/*.csv
"""
NextFlow From line 1718 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r cfmid_pos.zip all

aggregateMetfrag.r \\
    inputs=cfmid_pos.zip \\
    realNames=cfmid_pos.zip \\
    output=aggregated_identification_cfmid_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_cfmid_pos.csv
"""
NextFlow From line 1757 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=Jaccard_Score \\
        output=pep_identification_cfmid_pos.csv \\
        readTable=T
else
    touch pep_identification_cfmid_pos.csv
fi
"""
NextFlow From line 1789 of 1.0.1/main.nf 
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"""
if [ -s $cfmid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$cfmid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_cfmid.txt \\
        outputVariables=varsPOSout_pos_cfmid.txt \\
        outputMetaData=metadataPOSout_pos_cfmid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_cfmid.txt  \\
        outputVariables=varsPOSout_pos_cfmid.txt \\
        outputMetaData=metadataPOSout_pos_cfmid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1821 of 1.0.1/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 1907 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 1930 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 1953 of 1.0.1/main.nf 
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"""
touch quant_params_library_pos.json
touch rt_params_library_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    response_l=$params.ipo_response_l_library_pos \\
    response_h=$params.ipo_response_h_library_pos \\
    distFunc=$params.ipo_distFunc_library_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_library_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_library_pos \\
    factorGap_l=$params.ipo_factorGap_l_library_pos  \\
    factorGap_h=$params.ipo_factorGap_h_library_pos \\
    localAlignment=$params.ipo_localAlignment_library_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_library_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_library_pos \\
    bw_l=$params.ipo_bw_l_library_pos \\
    bw_h=$params.ipo_bw_h_library_pos \\
    minfrac_l=$params.ipo_minfrac_l_library_pos  \\
    minfrac_h=$params.ipo_minfrac_h_library_pos \\
    mzwid_l=$params.ipo_mzwid_l_library_pos \\
    mzwid_h=$params.ipo_mzwid_h_library_pos \\
    minsamp_l=$params.ipo_minsamp_l_library_pos  \\
    minsamp_h=$params.ipo_minsamp_h_library_pos \\
    max_l=$params.ipo_max_l_library_pos \\
    max_h=$params.ipo_max_h_library_pos \\
    ncores=$params.ipo_ncores_library_pos \\
    outputxset=quant_params_library_pos.json \\
    outputrt=rt_params_library_pos.json
"""
NextFlow IPO From line 1987 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_pos_xcms \\
    noise=$params.noise_quant_library_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_pos_xcms  \\
    mzdiff=$params.mzdiff_quant_library_pos_xcms \\
    snthresh=$params.snthresh_quant_library_pos_xcms \\
    prefilter_l=$params.prefilter_quant_library_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_pos_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_pos_xcms \\
    integrate=$params.integrate_quant_library_pos_xcms \\
    fitgauss=$params.fitgauss_quant_library_pos_xcms  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    ipo_inv=$ipo_library_pos_localQ \\
    $filter_argument
"""
NextFlow From line 2065 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 2131 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 2152 of 1.0.1/main.nf 
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"""
touch quant_params_library_pos.json
touch rt_params_library_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos  \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    response_l=$params.ipo_response_l_library_pos \\
    response_h=$params.ipo_response_h_library_pos \\
    distFunc=$params.ipo_distFunc_library_pos  \\
    factorDiag_l=$params.ipo_factorDiag_l_library_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_library_pos \\
    factorGap_l=$params.ipo_factorGap_l_library_pos  \\
    factorGap_h=$params.ipo_factorGap_h_library_pos \\
    localAlignment=$params.ipo_localAlignment_library_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_pos  \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_library_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_library_pos  \\
    bw_l=$params.ipo_bw_l_library_pos \\
    bw_h=$params.ipo_bw_h_library_pos \\
    minfrac_l=$params.ipo_minfrac_l_library_pos  \\
    minfrac_h=$params.ipo_minfrac_h_library_pos \\
    mzwid_l=$params.ipo_mzwid_l_library_pos \\
    mzwid_h=$params.ipo_mzwid_h_library_pos \\
    minsamp_l=$params.ipo_minsamp_l_library_pos  \\
    minsamp_h=$params.ipo_minsamp_h_library_pos \\
    max_l=$params.ipo_max_l_library_pos \\
    max_h=$params.ipo_max_h_library_pos \\
    ncores=$params.ipo_ncores_library_pos \\
    outputxset=quant_params_library_pos.json \\
    outputrt=rt_params_library_pos.json
"""
NextFlow IPO From line 2187 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_pos_xcms \\
    noise=$params.noise_quant_library_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_pos_xcms  \\
    mzdiff=$params.mzdiff_quant_library_pos_xcms \\
    snthresh=$params.snthresh_quant_library_pos_xcms \\
    prefilter_l=$params.prefilter_quant_library_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_pos_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_pos_xcms \\
    integrate=$params.integrate_quant_library_pos_xcms \\
    fitgauss=$params.fitgauss_quant_library_pos_xcms  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    ipo_inv=$ipo_library_pos_localQ \\
    $filter_argument
"""
NextFlow From line 2266 of 1.0.1/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=${rdata_files.baseName}.rdata
"""
NextFlow From line 2332 of 1.0.1/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    sigma=$params.sigma_group_library_pos_camera \\
    perfwhm=$params.perfwhm_group_library_pos_camera \\
    intval=$params.intval_group_library_pos_camera
"""
NextFlow From line 2353 of 1.0.1/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    ppm=$params.ppm_findaddcuts_library_pos_camera \\
    polarity=$params.polarity_findaddcuts_library_pos_camera
"""
NextFlow From line 2380 of 1.0.1/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    maxcharge=$params.maxcharge_findisotopes_library_pos_camera
"""
NextFlow From line 2406 of 1.0.1/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}_ReadMsmsLibrary.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 2432 of 1.0.1/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=${rdata_files_ms1.baseName}_MapMsms2Camera_library_pos.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_library_pos_msnbase \\
    rt=$params.rt_mapmsmstocamera_library_pos_msnbase
"""
NextFlow From line 2462 of 1.0.1/main.nf 
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"""
mkdir out

createLibrary.r \\
    inputCAMERA=$rdata_camera \\
    precursorppm=$params.ppm_create_library_pos_msnbase \\
    inputMS2=$ms2_data \\
    output=${rdata_camera.baseName}.csv \\
    inputLibrary=$library_desc  \\
    rawFileName=$params.raw_file_name_preparelibrary_pos_msnbase \\
    compundID=$params.compund_id_preparelibrary_pos_msnbase \\
    compoundName=$params.compound_name_preparelibrary_pos_msnbase  \\
    mzCol=$params.mz_col_preparelibrary_pos_msnbase \\
    whichmz=$params.which_mz_preparelibrary_pos_msnbase
"""
NextFlow From line 2494 of 1.0.1/main.nf 
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"""
collectLibrary.r \\
    inputs=$aggregatecdlibrary \\
    realNames=$aggregatecdlibrary \\
    output=library_pos.csv
"""
NextFlow From line 2530 of 1.0.1/main.nf 
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"""
#!env Rscript
Files<-list.files(,pattern = "zip",full.names=T)
Files_org<-list.files(,pattern = "zip")
for(f in Files){
    zip::unzip(zipfile = f,junkpaths = T)
}
Files<-list.files(,pattern = "txt",full.names=T)
FilesTMP<-sapply(strsplit(split = "_",fixed = T,x = basename(Files)),function(x){paste(x[-1],collapse = "_")})
    FileDub<-Files[duplicated(FilesTMP)]
for(x in FileDub){
    file.remove(x)
}
files_to_pass<-list.files(pattern="txt")
files_to_pass<-files_to_pass[!files_to_pass%in%Files_org]
zip::zip(zipfile="mappedtometfrag_pos.zip",files=files_to_pass)
"""
NextFlow From line 2555 of 1.0.1/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_pos.csv \\
    -th "-1" \\
    -im pos \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_pos_msnbase

sed -i '/^\$/d' aggregated_identification_library_pos.csv
"""
NextFlow From line 2593 of 1.0.1/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_pos.csv \\
    -th "-1" \\
    -im pos \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_pos_msnbase

sed -i '/^\$/d' aggregated_identification_library_pos.csv
"""
NextFlow From line 2627 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_library_pos.csv \\
        readTable=T
else
    touch pep_identification_library_pos.csv
fi
"""
NextFlow From line 2659 of 1.0.1/main.nf 
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"""
if [ -s $library_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$library_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
        combineReplicate=$params.combine_replicate_output_pos_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera  \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_library.txt \\
        outputVariables=varsPOSout_pos_library.txt \\
        outputMetaData=metadataPOSout_pos_library.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score  \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera  \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_library.txt \\
        outputVariables=varsPOSout_pos_library.txt \\
        outputMetaData=metadataPOSout_pos_library.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 2692 of 1.0.1/main.nf 
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"""
prepareOutput.r \\
    inputcamera=$camera_input_quant \\
    inputpheno=$phenotype_file \\
    ppm=$params.ppm_output_pos_camera \\
    rt=$params.rt_output_pos_camera  \\
    higherTheBetter=true \\
    scoreColumn=score \\
    impute=$params.impute_output_pos_camera \\
    typeColumn=$params.type_column_output_pos_camera \\
    selectedType=$params.selected_type_output_pos_camera  \\
    rename=$params.rename_output_pos_camera \\
    renameCol=$params.rename_col_output_pos_camera \\
    onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
    combineReplicate=$params.combine_replicate_output_pos_camera \\
    combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
    log=$params.log_output_pos_camera  \\
    sampleCoverage=$params.sample_coverage_output_pos_camera \\
    outputPeakTable=peaktablePOSout_POS_noid.txt \\
    outputVariables=varsPOSout_pos_noid.txt \\
    outputMetaData=metadataPOSout_pos_noid.txt \\
    Ifnormalize=$params.normalize_output_pos_camera
"""
NextFlow From line 2764 of 1.0.1/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 2816 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 2844 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 2866 of 1.0.1/main.nf 
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"""
touch quant_params_neg.json
touch rt_params_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_neg_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_neg \\
    columnToSelect=$params.ipo_columnToSelect_neg  \\
    valueToSelect=$params.ipo_valueToSelect_neg \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ncores=$params.ipo_ncores_neg \\
    outputxset=quant_params_neg.json \\
    outputrt=rt_params_neg.json
"""
NextFlow IPO From line 2902 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_neg_xcms \\
    noise=$params.noise_quant_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg  \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    mzdiff=$params.mzdiff_quant_neg_xcms \\
    snthresh=$params.snthresh_quant_neg_xcms \\
    prefilter_l=$params.prefilter_quant_neg_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_neg_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_neg_xcms \\
    integrate=$params.integrate_quant_neg_xcms \\
    fitgauss=$params.fitgauss_quant_neg_xcms  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    ipo_inv=$ipo_neg_localQ \\
    $filter_argument
"""
NextFlow From line 2987 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 3057 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 3079 of 1.0.1/main.nf 
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"""
touch quant_params_neg.json
touch rt_params_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_neg_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_neg \\
    columnToSelect=$params.ipo_columnToSelect_neg  \\
    valueToSelect=$params.ipo_valueToSelect_neg \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ncores=$params.ipo_ncores_neg \\
    outputxset=quant_params_neg.json \\
    outputrt=rt_params_neg.json
"""
NextFlow IPO From line 3115 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_neg_xcms \\
    noise=$params.noise_quant_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg  \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    mzdiff=$params.mzdiff_quant_neg_xcms \\
    snthresh=$params.snthresh_quant_neg_xcms \\
    prefilter_l=$params.prefilter_quant_neg_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_neg_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_neg_xcms \\
    integrate=$params.integrate_quant_neg_xcms \\
    fitgauss=$params.fitgauss_quant_neg_xcms  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    ipo_inv=$ipo_neg_localQ \\
    $filter_argument
"""
NextFlow From line 3200 of 1.0.1/main.nf 
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"""
nextFlowDIR=\$PWD
xcmsCollect.r input=$inputs_aggregated output=collection_neg.rdata
"""
NextFlow From line 3267 of 1.0.1/main.nf 
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"""
retCor.r \\
    input=\$PWD/$rdata_files \\
    output=RTcorrected_neg.rdata \\
    method=obiwarp \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ipo_inv=$ipo_neg_localRT \\
    ncores=$params.ipo_ncores_neg  \\
    profStep=$params.profStep_align_N1_neg_xcms \\
    center=$params.center_align_N1_neg_xcms \\
    response=$params.response_align_N1_neg_xcms  \\
    distFunc=$params.distFunc_align_N1_neg_xcms \\
    gapInit=$params.gapInit_align_N1_neg_xcms \\
    gapExtend=$params.gapExtend_align_N1_neg_xcms  \\
    factorDiag=$params.factorDiag_align_N1_neg_xcms \\
    factorGap=$params.factorGap_align_N1_neg_xcms \\
    localAlignment=$params.localAlignment_align_N1_neg_xcms \\
    $filter_argument \\
    inputraw=$inputs_aggregated
"""
NextFlow From line 3294 of 1.0.1/main.nf 
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"""
group.r \\
    input=$rdata_files \\
    output=groupN1_neg.rdata \\
    bandwidth=$params.bandwidth_group_N1_neg_xcms \\
    minfrac=$params.minfrac_group_N1_neg_xcms \\
    minsamp=$params.minsamp_group_N1_neg_xcms \\
    max=$params.max_group_N1_neg_xcms  \\
    mzwid=$params.mzwid_group_N1_neg_xcms
"""
NextFlow From line 3354 of 1.0.1/main.nf 
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"""
blankfilter.r \\
    input=$rdata_files \\
    output=blankFiltered_neg.rdata \\
    method=$params.method_blankfilter_neg_xcms \\
    blank=$params.blank_blankfilter_neg_xcms \\
    sample=$params.sample_blankfilter_neg_xcms \\
    rest=$params.rest_blankfilter_neg_xcms
"""
NextFlow From line 3386 of 1.0.1/main.nf 
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"""
dilutionfilter.r \\
    input=$rdata_files \\
    output=dilutionFiltered_neg.rdata \\
    Corto=$params.corto_dilutionfilter_neg_xcms  \\
    dilution=$params.dilution_dilutionfilter_neg_xcms \\
    pvalue=$params.pvalue_dilutionfilter_neg_xcms \\
    corcut=$params.corcut_dilutionfilter_neg_xcms \\
    abs=$params.abs_dilutionfilter_neg_xcms
"""
NextFlow From line 3419 of 1.0.1/main.nf 
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"""
cvfilter.r \\
    input=$rdata_files \\
    output=cvFiltered_neg.rdata \\
    qc=$params.qc_cvfilter_neg_xcms \\
    cvcut=$params.cvcut_cvfilter_neg_xcms
"""
NextFlow From line 3452 of 1.0.1/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=CameraAnnotatePeaks_neg.rdata
"""
NextFlow From line 3481 of 1.0.1/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=CameraGroup_neg.rdata \\
    sigma=$params.sigma_group_neg_camera \\
    perfwhm=$params.perfwhm_group_neg_camera \\
    intval=$params.intval_group_neg_camera
"""
NextFlow From line 3502 of 1.0.1/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=CameraFindAdducts_neg.rdata \\
    ppm=$params.ppm_findaddcuts_neg_camera \\
    polarity=$params.polarity_findaddcuts_neg_camera
"""
NextFlow From line 3528 of 1.0.1/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=CameraFindIsotopes_neg.rdata \\
    maxcharge=$params.maxcharge_findisotopes_neg_camera
"""
NextFlow From line 3553 of 1.0.1/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 3584 of 1.0.1/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$input_args \\
    output=MapMsms2Camera_neg.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_neg_msnbase \\
    rt=$params.rt_mapmsmstocamera_neg_msnbase
"""
NextFlow From line 3611 of 1.0.1/main.nf 
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"""
mkdir out

MS2ToMetFrag.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=out \\
    precursorppm=$params.precursorppm_msmstoparam_neg_msnbase  \\
    fragmentppm=$params.fragmentppm_msmstoparam_neg_msnbase \\
    fragmentabs=$params.fragmentabs_msmstoparam_neg_msnbase \\
    database=$params.database_msmstoparam_neg_msnbase  \\
    mode=$params.mode_msmstoparam_neg_msnbase \\
    adductRules=$params.adductRules_msmstoparam_neg_msnbase \\
    minPeaks=$params.minPeaks_msmstoparam_neg_msnbase

ls out/ -A -1  | cut -d'_' -f4- | tr ' ' '\n' | sort -u | xargs -I %  find out/ -type f -iname *% -exec zip %.zip {} +
"""
NextFlow From line 3638 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}_class_Csifingerid_neg.csv

fingerID.r \\
    input=\$PWD/inputs \\
    database=$params.database_csifingerid_neg_csifingerid \\
    tryOffline=T \\
    output=\$PWD/outputs/ \\
    ncores=$params.ncore_csifingerid_neg_csifingerid  \\
    timeout=$params.timeout_csifingerid_neg_csifingerid \\
    canopus=T \\
    canopusOutput=\$PWD/${parameters.baseName}_class_Csifingerid_neg.csv

zip -j -r ${parameters.baseName}_Csifingerid_neg.zip outputs/*.csv
"""
NextFlow From line 3682 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r Csifingerid_neg.zip all

aggregateMetfrag.r \\
    inputs=Csifingerid_neg.zip \\
    realNames=Csifingerid_neg.zip \\
    output=aggregated_identification_csifingerid_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_csifingerid_neg.csv
"""
NextFlow From line 3717 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_csifingerid_neg.csv \\
        readTable=T
else
    touch pep_identification_csifingerid_neg.csv
fi
"""
NextFlow From line 3751 of 1.0.1/main.nf 
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"""
if [ -s $csifingerid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$csifingerid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera  \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_csifingerid.txt  \\
        outputVariables=varsNEGout_neg_csifingerid.txt \\
        outputMetaData=metadataNEGout_neg_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera  \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_csifingerid.txt \\
        outputVariables=varsNEGout_neg_csifingerid.txt  \\
        outputMetaData=metadataNEGout_neg_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 3782 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_neg_metfrag \\
        run_metfrag.sh  \\
        -p {} \\
        -f \$PWD/outputs/{/.}.csv \\
        -l "\$PWD/$metfrag_database" \\
        -s "OfflineMetFusionScore"
zip -j -r ${parameters.baseName}_metfrag_neg.zip outputs/*.csv
"""
NextFlow From line 3878 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r metfrag_neg.zip all

aggregateMetfrag.r \\
    inputs=metfrag_neg.zip \\
    realNames=metfrag_neg.zip \\
    output=aggregated_identification_metfrag_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_metfrag_neg.csv
"""
NextFlow From line 3911 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=FragmenterScore \\
        output=pep_identification_metfrag_neg.csv \\
        readTable=T
else
    touch pep_identification_metfrag_neg.csv
fi
"""
NextFlow From line 3943 of 1.0.1/main.nf 
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"""
if [ -s $metfrag_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$metfrag_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera  \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_metfrag.txt  \\
        outputVariables=varsNEGout_neg_metfrag.txt \\
        outputMetaData=metadataNEGout_neg_metfrag.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera  \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_metfrag.txt \\
        outputVariables=varsNEGout_neg_metfrag.txt \\
        outputMetaData=metadataNEGout_neg_metfrag.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 3975 of 1.0.1/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv

find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_neg_cfmid \\
        cfmid.r \\
        input={} \\
        realName={/} \\
        databaseFile=\$PWD/$cfmid_database \\
        output=\$PWD/outputs/{/.}.csv \\
        candidate_id=$params.candidate_id_identification_neg_cfmid \\
        candidate_inchi_smiles=$params.candidate_inchi_smiles_identification_neg_cfmid  \\
        candidate_mass=$params.candidate_mass_identification_neg_cfmid \\
        databaseNameColumn=$params.database_name_column_identification_neg_cfmid \\
        databaseInChIColumn=$params.database_inchI_column_identification_neg_cfmid \\
        scoreType=Jaccard

zip -j -r ${parameters.baseName}_cfmid_neg.zip outputs/*.csv
"""
NextFlow From line 4060 of 1.0.1/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r cfmid_neg.zip all

aggregateMetfrag.r \\
    inputs=cfmid_neg.zip \\
    realNames=cfmid_neg.zip \\
    output=aggregated_identification_cfmid_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_cfmid_neg.csv
"""
NextFlow From line 4101 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=Jaccard_Score \\
        output=pep_identification_cfmid_neg.csv \\
        readTable=T
else
    touch pep_identification_cfmid_neg.csv
fi
"""
NextFlow From line 4134 of 1.0.1/main.nf 
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"""
if [ -s $cfmid_input_identification ]; then
    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$cfmid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_cfmid.txt  \\
        outputVariables=varsNEGout_neg_cfmid.txt \\
        outputMetaData=metadataNEGout_neg_cfmid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera  \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_cfmid.txt \\
        outputVariables=varsNEGout_neg_cfmid.txt \\
        outputMetaData=metadataNEGout_neg_cfmid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 4166 of 1.0.1/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 4244 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 4267 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 4288 of 1.0.1/main.nf 
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"""
touch quant_params_library_neg.json
touch rt_params_library_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    response_l=$params.ipo_response_l_library_neg \\
    response_h=$params.ipo_response_h_library_neg \\
    distFunc=$params.ipo_distFunc_library_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_library_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_library_neg \\
    factorGap_l=$params.ipo_factorGap_l_library_neg  \\
    factorGap_h=$params.ipo_factorGap_h_library_neg \\
    localAlignment=$params.ipo_localAlignment_library_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_library_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_library_neg \\
    bw_l=$params.ipo_bw_l_library_neg \\
    bw_h=$params.ipo_bw_h_library_neg \\
    minfrac_l=$params.ipo_minfrac_l_library_neg  \\
    minfrac_h=$params.ipo_minfrac_h_library_neg \\
    mzwid_l=$params.ipo_mzwid_l_library_neg \\
    mzwid_h=$params.ipo_mzwid_h_library_neg \\
    minsamp_l=$params.ipo_minsamp_l_library_neg  \\
    minsamp_h=$params.ipo_minsamp_h_library_neg \\
    max_l=$params.ipo_max_l_library_neg \\
    max_h=$params.ipo_max_h_library_neg \\
    ncores=$params.ipo_ncores_library_neg \\
    outputxset=quant_params_library_neg.json \\
    outputrt=rt_params_library_neg.json
"""
NextFlow IPO From line 4322 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_neg_xcms \\
    noise=$params.noise_quant_library_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_neg_xcms  \\
    mzdiff=$params.mzdiff_quant_library_neg_xcms \\
    snthresh=$params.snthresh_quant_library_neg_xcms \\
    prefilter_l=$params.prefilter_quant_library_neg_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_neg_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_neg_xcms \\
    integrate=$params.integrate_quant_library_neg_xcms \\
    fitgauss=$params.fitgauss_quant_library_neg_xcms  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    ipo_inv=$ipo_library_neg_localQ \\
    $filter_argument
"""
NextFlow From line 4401 of 1.0.1/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 4467 of 1.0.1/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 4488 of 1.0.1/main.nf 
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"""
touch quant_params_library_neg.json
touch rt_params_library_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    response_l=$params.ipo_response_l_library_neg \\
    response_h=$params.ipo_response_h_library_neg \\
    distFunc=$params.ipo_distFunc_library_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_library_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_library_neg \\
    factorGap_l=$params.ipo_factorGap_l_library_neg  \\
    factorGap_h=$params.ipo_factorGap_h_library_neg \\
    localAlignment=$params.ipo_localAlignment_library_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_library_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_library_neg \\
    bw_l=$params.ipo_bw_l_library_neg \\
    bw_h=$params.ipo_bw_h_library_neg \\
    minfrac_l=$params.ipo_minfrac_l_library_neg  \\
    minfrac_h=$params.ipo_minfrac_h_library_neg \\
    mzwid_l=$params.ipo_mzwid_l_library_neg \\
    mzwid_h=$params.ipo_mzwid_h_library_neg \\
    minsamp_l=$params.ipo_minsamp_l_library_neg  \\
    minsamp_h=$params.ipo_minsamp_h_library_neg \\
    max_l=$params.ipo_max_l_library_neg \\
    max_h=$params.ipo_max_h_library_neg \\
    ncores=$params.ipo_ncores_library_neg \\
    outputxset=quant_params_library_neg.json \\
    outputrt=rt_params_library_neg.json
"""
NextFlow IPO From line 4521 of 1.0.1/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_neg_xcms \\
    noise=$params.noise_quant_library_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_neg_xcms  \\
    mzdiff=$params.mzdiff_quant_library_neg_xcms \\
    snthresh=$params.snthresh_quant_library_neg_xcms \\
    prefilter_l=$params.prefilter_quant_library_neg_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_neg_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_neg_xcms \\
    integrate=$params.integrate_quant_library_neg_xcms \\
    fitgauss=$params.fitgauss_quant_library_neg_xcms  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    ipo_inv=$ipo_library_neg_localQ \\
    $filter_argument
"""
NextFlow From line 4600 of 1.0.1/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=${rdata_files.baseName}.rdata
"""
NextFlow From line 4664 of 1.0.1/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    sigma=$params.sigma_group_library_neg_camera \\
    perfwhm=$params.perfwhm_group_library_neg_camera \\
    intval=$params.intval_group_library_neg_camera
"""
NextFlow From line 4685 of 1.0.1/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    ppm=$params.ppm_findaddcuts_library_neg_camera \\
    polarity=$params.polarity_findaddcuts_library_neg_camera
"""
NextFlow From line 4711 of 1.0.1/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    maxcharge=$params.maxcharge_findisotopes_library_neg_camera
"""
NextFlow From line 4737 of 1.0.1/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}_ReadMsmsLibrary.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 4761 of 1.0.1/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=${rdata_files_ms1.baseName}_MapMsms2Camera_library_neg.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_library_neg_msnbase \\
    rt=$params.rt_mapmsmstocamera_library_neg_msnbase
"""
NextFlow From line 4790 of 1.0.1/main.nf 
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"""
mkdir out
createLibrary.r \\
    inputCAMERA=$rdata_camera \\
    precursorppm=$params.ppm_create_library_neg_msnbase \\
    inputMS2=$ms2_data \\
    output=${rdata_camera.baseName}.csv  \\
    inputLibrary=$library_desc \\
    rawFileName=$params.raw_file_name_preparelibrary_neg_msnbase \\
    compundID=$params.compund_id_preparelibrary_neg_msnbase  \\
    compoundName=$params.compound_name_preparelibrary_neg_msnbase \\
    mzCol=$params.mz_col_preparelibrary_neg_msnbase \\
    whichmz=$params.which_mz_preparelibrary_neg_msnbase
"""
NextFlow From line 4822 of 1.0.1/main.nf 
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"""
collectLibrary.r \\
    inputs=$aggregatecdlibrary \\
    realNames=$aggregatecdlibrary \\
    output=library_neg.csv
"""
NextFlow From line 4855 of 1.0.1/main.nf 
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"""
#!env Rscript
Files<-list.files(,pattern = "zip",full.names=T)
Files_org<-list.files(,pattern = "zip")
for(f in Files){
    zip::unzip(zipfile = f,junkpaths = T)
}
Files<-list.files(,pattern = "txt",full.names=T)
FilesTMP<-sapply(strsplit(split = "_",fixed = T,x = basename(Files)),function(x){paste(x[-1],collapse = "_")})
FileDub<-Files[duplicated(FilesTMP)]
for(x in FileDub){
    file.remove(x)
}
files_to_pass<-list.files(pattern="txt")
files_to_pass<-files_to_pass[!files_to_pass%in%Files_org]
zip::zip(zipfile="mappedtometfrag_neg.zip",files=files_to_pass)
"""
NextFlow From line 4879 of 1.0.1/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters  \\
    -out aggregated_identification_library_neg.csv \\
    -th "-1" \\
    -im neg  \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_neg_msnbase
sed -i '/^\$/d' aggregated_identification_library_neg.csv
"""
NextFlow From line 4918 of 1.0.1/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_neg.csv \\
    -th "-1" \\
    -im neg \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_neg_msnbase
sed -i '/^\$/d' aggregated_identification_library_neg.csv
"""
NextFlow From line 4950 of 1.0.1/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_library_neg.csv \\
        readTable=T
else
    touch pep_identification_library_neg.csv
fi
"""
NextFlow From line 4981 of 1.0.1/main.nf 
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"""
if [ -s $library_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$library_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera  \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_library.txt  \\
        outputVariables=varsNEGout_neg_library.txt \\
        outputMetaData=metadataNEGout_neg_library.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file  \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true  \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera  \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera  \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera  \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera  \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_library.txt  \\
        outputVariables=varsNEGout_neg_library.txt \\
        outputMetaData=metadataNEGout_neg_library.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 5014 of 1.0.1/main.nf 
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"""
prepareOutput.r \\
    inputcamera=$camera_input_quant \\
    inputpheno=$phenotype_file \\
    ppm=$params.ppm_output_neg_camera \\
    rt=$params.rt_output_neg_camera \\
    higherTheBetter=true \\
    scoreColumn=score  \\
    impute=$params.impute_output_neg_camera \\
    typeColumn=$params.type_column_output_neg_camera \\
    selectedType=$params.selected_type_output_neg_camera \\
    rename=$params.rename_output_neg_camera  \\
    renameCol=$params.rename_col_output_neg_camera \\
    onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
    combineReplicate=$params.combine_replicate_output_neg_camera  \\
    combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
    log=$params.log_output_neg_camera \\
    sampleCoverage=$params.sample_coverage_output_neg_camera  \\
    outputPeakTable=peaktableNEGout_NEG_noid.txt \\
    outputVariables=varsNEGout_neg_noid.txt \\
    outputMetaData=metadataNEGout_neg_noid.txt \\
    Ifnormalize=$params.normalize_output_neg_camera
"""
NextFlow From line 5086 of 1.0.1/main.nf 
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"""

echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
Rscript -e "cat(as.character(packageVersion('CAMERA')),'\\n')" &> v_camera.txt
Rscript -e "cat(as.character(packageVersion('xcms')),'\\n')" &> v_xcms.txt
Rscript -e "cat(as.character(packageVersion('MSnbase')),'\\n')" &> v_msnbase.txt
Rscript -e "cat(as.character(packageVersion('IPO')),'\\n')" &> v_ipo.txt
OpenMSInfo |  grep -oP -m 1 '([0-9][.][0-9][.][0-9])' &> v_openms.txt
sh /usr/bin/CSI/bin/sirius.sh --loglevel=OFF --version 2>1 | grep -oP -m 1 '([0-9][.][0-9][.][0-9])' &> v_sirius.txt

scrape_software_versions.py &> software_versions_mqc.yaml
"""
NextFlow From line 423 of master/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 463 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 492 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 516 of master/main.nf 
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"""
touch quant_params_pos.json
touch rt_params_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_pos_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_pos \\
    columnToSelect=$params.ipo_columnToSelect_pos  \\
    valueToSelect=$params.ipo_valueToSelect_pos \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ncores=$params.ipo_ncores_pos \\
    outputxset=quant_params_pos.json \\
    outputrt=rt_params_pos.json
"""
NextFlow IPO From line 554 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_pos_xcms \\
    noise=$params.noise_quant_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    mzdiff=$params.mzdiff_quant_pos_xcms \\
    snthresh=$params.snthresh_quant_pos_xcms  \\
    prefilter_l=$params.prefilter_quant_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_pos_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_pos_xcms \\
    integrate=$params.integrate_quant_pos_xcms  \\
    fitgauss=$params.fitgauss_quant_pos_xcms \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos  \\
    mzCenterFun=$params.ipo_mzCenterFun_pos \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    ipo_inv=$ipo_pos_localQ \\
    $filter_argument
"""
NextFlow From line 639 of master/main.nf 
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FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 710 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos  \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 733 of master/main.nf 
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"""
touch quant_params_pos.json
touch rt_params_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_pos_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_pos \\
    columnToSelect=$params.ipo_columnToSelect_pos  \\
    valueToSelect=$params.ipo_valueToSelect_pos \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ncores=$params.ipo_ncores_pos \\
    outputxset=quant_params_pos.json \\
    outputrt=rt_params_pos.json
"""
NextFlow IPO From line 769 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_pos_xcms \\
    peakwidthHigh=$params.peakwidthhigh_quant_pos_xcms  \\
    noise=$params.noise_quant_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_pos  \\
    sampleClass=$params.sampleclass_quant_pos_xcms \\
    mzdiff=$params.mzdiff_quant_pos_xcms \\
    snthresh=$params.snthresh_quant_pos_xcms \\
    prefilter_l=$params.prefilter_quant_pos_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_pos_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_pos_xcms \\
    integrate=$params.integrate_quant_pos_xcms  \\
    fitgauss=$params.fitgauss_quant_pos_xcms \\
    methodXset=$params.ipo_methodXset_pos \\
    methodRT=$params.ipo_methodRT_pos \\
    noise_l=$params.ipo_noise_l_pos  \\
    noise_h=$params.ipo_noise_h_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_pos  \\
    snthresh_l=$params.ipo_snthresh_l_pos \\
    snthresh_h=$params.ipo_snthresh_h_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_pos  \\
    integrate=$params.ipo_integrate_pos \\
    fitgauss=$params.ipo_fitgauss_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_pos  \\
    ipo_inv=$ipo_pos_localQ \\
    $filter_argument
"""
NextFlow From line 854 of master/main.nf 
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"""
nextFlowDIR=\$PWD
xcmsCollect.r input=$inputs_aggregated output=collection_pos.rdata
"""
NextFlow From line 921 of master/main.nf 
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"""
retCor.r \\
    input=\$PWD/$rdata_files \\
    output=RTcorrected_pos.rdata \\
    method=obiwarp \\
    response_l=$params.ipo_response_l_pos \\
    response_h=$params.ipo_response_h_pos \\
    distFunc=$params.ipo_distFunc_pos  \\
    factorDiag_l=$params.ipo_factorDiag_l_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_pos \\
    factorGap_l=$params.ipo_factorGap_l_pos  \\
    factorGap_h=$params.ipo_factorGap_h_pos \\
    localAlignment=$params.ipo_localAlignment_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_pos \\
    bw_l=$params.ipo_bw_l_pos \\
    bw_h=$params.ipo_bw_h_pos \\
    minfrac_l=$params.ipo_minfrac_l_pos  \\
    minfrac_h=$params.ipo_minfrac_h_pos \\
    mzwid_l=$params.ipo_mzwid_l_pos \\
    mzwid_h=$params.ipo_mzwid_h_pos \\
    minsamp_l=$params.ipo_minsamp_l_pos  \\
    minsamp_h=$params.ipo_minsamp_h_pos \\
    max_l=$params.ipo_max_l_pos \\
    max_h=$params.ipo_max_h_pos \\
    ipo_inv=$ipo_pos_localRT \\
    ncores=$params.ipo_ncores_pos  \\
    profStep=$params.profStep_align_N1_pos_xcms \\
    center=$params.center_align_N1_pos_xcms \\
    response=$params.response_align_N1_pos_xcms  \\
    distFunc=$params.distFunc_align_N1_pos_xcms \\
    gapInit=$params.gapInit_align_N1_pos_xcms \\
    gapExtend=$params.gapExtend_align_N1_pos_xcms  \\
    factorDiag=$params.factorDiag_align_N1_pos_xcms \\
    factorGap=$params.factorGap_align_N1_pos_xcms \\
    localAlignment=$params.localAlignment_align_N1_pos_xcms \\
    $filter_argument \\
    inputraw=$inputs_aggregated
"""
NextFlow From line 948 of master/main.nf 
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"""
group.r \\
    input=$rdata_files \\
    output=groupN1_pos.rdata \\
    bandwidth=$params.bandwidth_group_N1_pos_xcms \\
    minfrac=$params.minfrac_group_N1_pos_xcms \\
    minsamp=$params.minsamp_group_N1_pos_xcms \\
    max=$params.max_group_N1_pos_xcms  \\
    mzwid=$params.mzwid_group_N1_pos_xcms
"""
NextFlow From line 1010 of master/main.nf 
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"""
blankfilter.r \\
    input=$rdata_files \\
    output=blankFiltered_pos.rdata \\
    method=$params.method_blankfilter_pos_xcms \\
    blank=$params.blank_blankfilter_pos_xcms \\
    sample=$params.sample_blankfilter_pos_xcms \\
    rest=$params.rest_blankfilter_pos_xcms
"""
NextFlow From line 1042 of master/main.nf 
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"""
dilutionfilter.r \\
    input=$rdata_files \\
    output=dilutionFiltered_pos.rdata \\
    Corto=$params.corto_dilutionfilter_pos_xcms  \\
    dilution=$params.dilution_dilutionfilter_pos_xcms \\
    pvalue=$params.pvalue_dilutionfilter_pos_xcms \\
    corcut=$params.corcut_dilutionfilter_pos_xcms \\
    abs=$params.abs_dilutionfilter_pos_xcms
"""
NextFlow From line 1074 of master/main.nf 
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"""
cvfilter.r \\
    input=$rdata_files \\
    output=cvFiltered_pos.rdata \\
    qc=$params.qc_cvfilter_pos_xcms \\
    cvcut=$params.cvcut_cvfilter_pos_xcms
"""
NextFlow From line 1108 of master/main.nf 
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"""
xsAnnotate.r  input=$rdata_files output=CameraAnnotatePeaks_pos.rdata
"""
NextFlow From line 1137 of master/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=CameraGroup_pos.rdata \\
    sigma=$params.sigma_group_pos_camera \\
    perfwhm=$params.perfwhm_group_pos_camera \\
    intval=$params.intval_group_pos_camera
"""
NextFlow From line 1158 of master/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=CameraFindAdducts_pos.rdata \\
    ppm=$params.ppm_findaddcuts_pos_camera \\
    polarity=$params.polarity_findaddcuts_pos_camera
"""
NextFlow From line 1185 of master/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=CameraFindIsotopes_pos.rdata \\
    maxcharge=$params.maxcharge_findisotopes_pos_camera
"""
NextFlow From line 1210 of master/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 1241 of master/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$input_args \\
    output=MapMsms2Camera_pos.rdata \\
    ppm=$params.ppm_mapmsmstocamera_pos_msnbase \\
    rt=$params.rt_mapmsmstocamera_pos_msnbase
"""
NextFlow From line 1268 of master/main.nf 
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"""
mkdir out

MS2ToMetFrag.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=out  \\
    precursorppm=$params.precursorppm_msmstoparam_pos_msnbase \\
    fragmentppm=$params.fragmentppm_msmstoparam_pos_msnbase \\
    fragmentabs=$params.fragmentabs_msmstoparam_pos_msnbase  \\
    database=$params.database_msmstoparam_pos_msnbase \\
    mode=$params.mode_msmstoparam_pos_msnbase \\
    adductRules=$params.adductRules_msmstoparam_pos_msnbase \\
    minPeaks=$params.minPeaks_msmstoparam_pos_msnbase

ls out/ -A -1  | cut -d'_' -f4- | tr ' ' '\n' | sort -u | xargs -I %  find out/ -type f -iname *% -exec zip %.zip {} +
"""
NextFlow From line 1296 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}_class_Csifingerid_pos.csv

fingerID.r \\
    input=\$PWD/inputs \\
    database=$params.database_csifingerid_pos_csifingerid \\
    tryOffline=T  \\
    output=\$PWD/outputs/ \\
    ncores=$params.ncore_csifingerid_pos_csifingerid \\
    timeout=$params.timeout_csifingerid_pos_csifingerid \\
    canopus=T \\
    canopusOutput=\$PWD/${parameters.baseName}_class_Csifingerid_pos.csv

zip -j -r ${parameters.baseName}_Csifingerid_pos.zip outputs/*.csv
"""
NextFlow From line 1341 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r Csifingerid_pos.zip all

aggregateMetfrag.r \\
    inputs=Csifingerid_pos.zip \\
    realNames=Csifingerid_pos.zip \\
    output=aggregated_identification_csifingerid_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_csifingerid_pos.csv
"""
NextFlow From line 1377 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_csifingerid_pos.csv \\
        readTable=T
else
    touch pep_identification_csifingerid_pos.csv
fi
"""
NextFlow From line 1410 of master/main.nf 
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"""
if [ -s $csifingerid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$csifingerid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_csifingerid.txt \\
        outputVariables=varsPOSout_pos_csifingerid.txt \\
        outputMetaData=metadataPOSout_pos_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_csifingerid.txt  \\
        outputVariables=varsPOSout_pos_csifingerid.txt \\
        outputMetaData=metadataPOSout_pos_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1440 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_pos_metfrag \\
        run_metfrag.sh \\
        -p {} \\
        -f \$PWD/outputs/{/.}.csv \\
        -l "\$PWD/$metfrag_database" \\
        -s "OfflineMetFusionScore"
zip -j -r ${parameters.baseName}_metfrag_pos.zip outputs/*.csv
"""
NextFlow From line 1536 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r metfrag_pos.zip all

aggregateMetfrag.r \\
    inputs=metfrag_pos.zip \\
    realNames=metfrag_pos.zip \\
    output=aggregated_identification_metfrag_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_metfrag_pos.csv
"""
NextFlow From line 1569 of master/main.nf 
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"""
if [ -s $identification_result ];then
    metfragPEP.r \\
        input=$identification_result \\
        score=FragmenterScore \\
        output=pep_identification_metfrag_pos.csv \\
        readTable=T
else
    touch pep_identification_metfrag_pos.csv
fi
"""
NextFlow From line 1601 of master/main.nf 
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"""
if [ -s $metfrag_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$metfrag_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
        combineReplicate=$params.combine_replicate_output_pos_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_metfrag.txt \\
        outputVariables=varsPOSout_pos_metfrag.txt \\
        outputMetaData=metadataPOSout_pos_metfrag.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore  \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera  \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_metfrag.txt \\
        outputVariables=varsPOSout_pos_metfrag.txt \\
        outputMetaData=metadataPOSout_pos_metfrag.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1633 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_pos_cfmid cfmid.r \\
        input={} \\
        realName={/} \\
        databaseFile=\$PWD/$cfmid_database  \\
        output=\$PWD/outputs/{/.}.csv \\
        candidate_id=$params.candidate_id_identification_pos_cfmid \\
        candidate_inchi_smiles=$params.candidate_inchi_smiles_identification_pos_cfmid \\
        candidate_mass=$params.candidate_mass_identification_pos_cfmid \\
        databaseNameColumn=$params.database_name_column_identification_pos_cfmid \\
        databaseInChIColumn=$params.database_inchI_column_identification_pos_cfmid \\
        scoreType=Jaccard

zip -j -r ${parameters.baseName}_cfmid_pos.zip outputs/*.csv
"""
NextFlow From line 1718 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r cfmid_pos.zip all

aggregateMetfrag.r \\
    inputs=cfmid_pos.zip \\
    realNames=cfmid_pos.zip \\
    output=aggregated_identification_cfmid_pos.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_cfmid_pos.csv
"""
NextFlow From line 1757 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=Jaccard_Score \\
        output=pep_identification_cfmid_pos.csv \\
        readTable=T
else
    touch pep_identification_cfmid_pos.csv
fi
"""
NextFlow From line 1789 of master/main.nf 
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"""
if [ -s $cfmid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$cfmid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_cfmid.txt \\
        outputVariables=varsPOSout_pos_cfmid.txt \\
        outputMetaData=metadataPOSout_pos_cfmid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera  \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_cfmid.txt  \\
        outputVariables=varsPOSout_pos_cfmid.txt \\
        outputMetaData=metadataPOSout_pos_cfmid.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 1821 of master/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 1907 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 1930 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 1953 of master/main.nf 
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"""
touch quant_params_library_pos.json
touch rt_params_library_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    response_l=$params.ipo_response_l_library_pos \\
    response_h=$params.ipo_response_h_library_pos \\
    distFunc=$params.ipo_distFunc_library_pos \\
    factorDiag_l=$params.ipo_factorDiag_l_library_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_library_pos \\
    factorGap_l=$params.ipo_factorGap_l_library_pos  \\
    factorGap_h=$params.ipo_factorGap_h_library_pos \\
    localAlignment=$params.ipo_localAlignment_library_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_pos \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_library_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_library_pos \\
    bw_l=$params.ipo_bw_l_library_pos \\
    bw_h=$params.ipo_bw_h_library_pos \\
    minfrac_l=$params.ipo_minfrac_l_library_pos  \\
    minfrac_h=$params.ipo_minfrac_h_library_pos \\
    mzwid_l=$params.ipo_mzwid_l_library_pos \\
    mzwid_h=$params.ipo_mzwid_h_library_pos \\
    minsamp_l=$params.ipo_minsamp_l_library_pos  \\
    minsamp_h=$params.ipo_minsamp_h_library_pos \\
    max_l=$params.ipo_max_l_library_pos \\
    max_h=$params.ipo_max_h_library_pos \\
    ncores=$params.ipo_ncores_library_pos \\
    outputxset=quant_params_library_pos.json \\
    outputrt=rt_params_library_pos.json
"""
NextFlow IPO From line 1987 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_pos_xcms \\
    noise=$params.noise_quant_library_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_pos_xcms  \\
    mzdiff=$params.mzdiff_quant_library_pos_xcms \\
    snthresh=$params.snthresh_quant_library_pos_xcms \\
    prefilter_l=$params.prefilter_quant_library_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_pos_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_pos_xcms \\
    integrate=$params.integrate_quant_library_pos_xcms \\
    fitgauss=$params.fitgauss_quant_library_pos_xcms  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    ipo_inv=$ipo_library_pos_localQ \\
    $filter_argument
"""
NextFlow From line 2065 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 2131 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=positive \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 2152 of master/main.nf 
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"""
touch quant_params_library_pos.json
touch rt_params_library_pos.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos  \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    response_l=$params.ipo_response_l_library_pos \\
    response_h=$params.ipo_response_h_library_pos \\
    distFunc=$params.ipo_distFunc_library_pos  \\
    factorDiag_l=$params.ipo_factorDiag_l_library_pos \\
    factorDiag_h=$params.ipo_factorDiag_h_library_pos \\
    factorGap_l=$params.ipo_factorGap_l_library_pos  \\
    factorGap_h=$params.ipo_factorGap_h_library_pos \\
    localAlignment=$params.ipo_localAlignment_library_pos \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_pos  \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_pos \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_pos  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_pos \\
    ipo_profStep_l=$params.ipo_profStep_l_library_pos \\
    ipo_profStep_h=$params.ipo_profStep_h_library_pos  \\
    bw_l=$params.ipo_bw_l_library_pos \\
    bw_h=$params.ipo_bw_h_library_pos \\
    minfrac_l=$params.ipo_minfrac_l_library_pos  \\
    minfrac_h=$params.ipo_minfrac_h_library_pos \\
    mzwid_l=$params.ipo_mzwid_l_library_pos \\
    mzwid_h=$params.ipo_mzwid_h_library_pos \\
    minsamp_l=$params.ipo_minsamp_l_library_pos  \\
    minsamp_h=$params.ipo_minsamp_h_library_pos \\
    max_l=$params.ipo_max_l_library_pos \\
    max_h=$params.ipo_max_h_library_pos \\
    ncores=$params.ipo_ncores_library_pos \\
    outputxset=quant_params_library_pos.json \\
    outputrt=rt_params_library_pos.json
"""
NextFlow IPO From line 2187 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_pos_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_pos_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_pos_xcms \\
    noise=$params.noise_quant_library_pos_xcms \\
    polarity=positive \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_pos_xcms  \\
    mzdiff=$params.mzdiff_quant_library_pos_xcms \\
    snthresh=$params.snthresh_quant_library_pos_xcms \\
    prefilter_l=$params.prefilter_quant_library_pos_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_pos_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_pos_xcms \\
    integrate=$params.integrate_quant_library_pos_xcms \\
    fitgauss=$params.fitgauss_quant_library_pos_xcms  \\
    methodXset=$params.ipo_methodXset_library_pos \\
    methodRT=$params.ipo_methodRT_library_pos \\
    noise_l=$params.ipo_noise_l_library_pos  \\
    noise_h=$params.ipo_noise_h_library_pos \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_pos \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_pos  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_pos \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_pos  \\
    snthresh_l=$params.ipo_snthresh_l_library_pos \\
    snthresh_h=$params.ipo_snthresh_h_library_pos \\
    mzCenterFun=$params.ipo_mzCenterFun_library_pos  \\
    integrate=$params.ipo_integrate_library_pos \\
    fitgauss=$params.ipo_fitgauss_library_pos \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_pos  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_pos \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_pos \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_pos \\
    ipo_ppm_l=$params.ipo_ppm_l_library_pos  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_pos \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_pos \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_pos \\
    ipo_charge_camera=$params.ipo_charge_camera_library_pos  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_pos  \\
    ipo_inv=$ipo_library_pos_localQ \\
    $filter_argument
"""
NextFlow From line 2266 of master/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=${rdata_files.baseName}.rdata
"""
NextFlow From line 2332 of master/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    sigma=$params.sigma_group_library_pos_camera \\
    perfwhm=$params.perfwhm_group_library_pos_camera \\
    intval=$params.intval_group_library_pos_camera
"""
NextFlow From line 2353 of master/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    ppm=$params.ppm_findaddcuts_library_pos_camera \\
    polarity=$params.polarity_findaddcuts_library_pos_camera
"""
NextFlow From line 2380 of master/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    maxcharge=$params.maxcharge_findisotopes_library_pos_camera
"""
NextFlow From line 2406 of master/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}_ReadMsmsLibrary.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 2432 of master/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=${rdata_files_ms1.baseName}_MapMsms2Camera_library_pos.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_library_pos_msnbase \\
    rt=$params.rt_mapmsmstocamera_library_pos_msnbase
"""
NextFlow From line 2462 of master/main.nf 
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"""
mkdir out

createLibrary.r \\
    inputCAMERA=$rdata_camera \\
    precursorppm=$params.ppm_create_library_pos_msnbase \\
    inputMS2=$ms2_data \\
    output=${rdata_camera.baseName}.csv \\
    inputLibrary=$library_desc  \\
    rawFileName=$params.raw_file_name_preparelibrary_pos_msnbase \\
    compundID=$params.compund_id_preparelibrary_pos_msnbase \\
    compoundName=$params.compound_name_preparelibrary_pos_msnbase  \\
    mzCol=$params.mz_col_preparelibrary_pos_msnbase \\
    whichmz=$params.which_mz_preparelibrary_pos_msnbase
"""
NextFlow From line 2494 of master/main.nf 
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"""
collectLibrary.r \\
    inputs=$aggregatecdlibrary \\
    realNames=$aggregatecdlibrary \\
    output=library_pos.csv
"""
NextFlow From line 2530 of master/main.nf 
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"""
#!env Rscript
Files<-list.files(,pattern = "zip",full.names=T)
Files_org<-list.files(,pattern = "zip")
for(f in Files){
    zip::unzip(zipfile = f,junkpaths = T)
}
Files<-list.files(,pattern = "txt",full.names=T)
FilesTMP<-sapply(strsplit(split = "_",fixed = T,x = basename(Files)),function(x){paste(x[-1],collapse = "_")})
    FileDub<-Files[duplicated(FilesTMP)]
for(x in FileDub){
    file.remove(x)
}
files_to_pass<-list.files(pattern="txt")
files_to_pass<-files_to_pass[!files_to_pass%in%Files_org]
zip::zip(zipfile="mappedtometfrag_pos.zip",files=files_to_pass)
"""
NextFlow From line 2555 of master/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_pos.csv \\
    -th "-1" \\
    -im pos \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_pos_msnbase

sed -i '/^\$/d' aggregated_identification_library_pos.csv
"""
NextFlow From line 2593 of master/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_pos.csv \\
    -th "-1" \\
    -im pos \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_pos_msnbase

sed -i '/^\$/d' aggregated_identification_library_pos.csv
"""
NextFlow From line 2627 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_library_pos.csv \\
        readTable=T
else
    touch pep_identification_library_pos.csv
fi
"""
NextFlow From line 2659 of master/main.nf 
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"""
if [ -s $library_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$library_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera  \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera  \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
        combineReplicate=$params.combine_replicate_output_pos_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera  \\
        sampleCoverage=$params.sample_coverage_output_pos_camera \\
        outputPeakTable=peaktablePOSout_pos_library.txt \\
        outputVariables=varsPOSout_pos_library.txt \\
        outputMetaData=metadataPOSout_pos_library.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_pos_camera \\
        rt=$params.rt_output_pos_camera \\
        higherTheBetter=true \\
        scoreColumn=score  \\
        impute=$params.impute_output_pos_camera \\
        typeColumn=$params.type_column_output_pos_camera \\
        selectedType=$params.selected_type_output_pos_camera \\
        rename=$params.rename_output_pos_camera  \\
        renameCol=$params.rename_col_output_pos_camera \\
        onlyReportWithID=$params.only_report_with_id_output_pos_camera \\
        combineReplicate=$params.combine_replicate_output_pos_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
        log=$params.log_output_pos_camera \\
        sampleCoverage=$params.sample_coverage_output_pos_camera  \\
        outputPeakTable=peaktablePOSout_pos_library.txt \\
        outputVariables=varsPOSout_pos_library.txt \\
        outputMetaData=metadataPOSout_pos_library.txt \\
        Ifnormalize=$params.normalize_output_pos_camera

fi
"""
NextFlow From line 2692 of master/main.nf 
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"""
prepareOutput.r \\
    inputcamera=$camera_input_quant \\
    inputpheno=$phenotype_file \\
    ppm=$params.ppm_output_pos_camera \\
    rt=$params.rt_output_pos_camera  \\
    higherTheBetter=true \\
    scoreColumn=score \\
    impute=$params.impute_output_pos_camera \\
    typeColumn=$params.type_column_output_pos_camera \\
    selectedType=$params.selected_type_output_pos_camera  \\
    rename=$params.rename_output_pos_camera \\
    renameCol=$params.rename_col_output_pos_camera \\
    onlyReportWithID=$params.only_report_with_id_output_pos_camera  \\
    combineReplicate=$params.combine_replicate_output_pos_camera \\
    combineReplicateColumn=$params.combine_replicate_column_output_pos_camera \\
    log=$params.log_output_pos_camera  \\
    sampleCoverage=$params.sample_coverage_output_pos_camera \\
    outputPeakTable=peaktablePOSout_POS_noid.txt \\
    outputVariables=varsPOSout_pos_noid.txt \\
    outputMetaData=metadataPOSout_pos_noid.txt \\
    Ifnormalize=$params.normalize_output_pos_camera
"""
NextFlow From line 2764 of master/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 2816 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 2844 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 2866 of master/main.nf 
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"""
touch quant_params_neg.json
touch rt_params_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_neg_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_neg \\
    columnToSelect=$params.ipo_columnToSelect_neg  \\
    valueToSelect=$params.ipo_valueToSelect_neg \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ncores=$params.ipo_ncores_neg \\
    outputxset=quant_params_neg.json \\
    outputrt=rt_params_neg.json
"""
NextFlow IPO From line 2902 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_neg_xcms \\
    noise=$params.noise_quant_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg  \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    mzdiff=$params.mzdiff_quant_neg_xcms \\
    snthresh=$params.snthresh_quant_neg_xcms \\
    prefilter_l=$params.prefilter_quant_neg_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_neg_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_neg_xcms \\
    integrate=$params.integrate_quant_neg_xcms \\
    fitgauss=$params.fitgauss_quant_neg_xcms  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    ipo_inv=$ipo_neg_localQ \\
    $filter_argument
"""
NextFlow From line 2987 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 3057 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    phenoFile=$phenotype_file  \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 3079 of master/main.nf 
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"""
touch quant_params_neg.json
touch rt_params_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=$ipo_neg_globalAvoidRT \\
    allSamples=$params.ipo_allSamples_neg \\
    columnToSelect=$params.ipo_columnToSelect_neg  \\
    valueToSelect=$params.ipo_valueToSelect_neg \\
    phenoFile=$phenotype_file  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ncores=$params.ipo_ncores_neg \\
    outputxset=quant_params_neg.json \\
    outputrt=rt_params_neg.json
"""
NextFlow IPO From line 3115 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_neg_xcms \\
    noise=$params.noise_quant_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    phenoFile=$phenotype_file \\
    phenoDataColumn=$params.phenodatacolumn_quant_neg  \\
    sampleClass=$params.sampleclass_quant_neg_xcms \\
    mzdiff=$params.mzdiff_quant_neg_xcms \\
    snthresh=$params.snthresh_quant_neg_xcms \\
    prefilter_l=$params.prefilter_quant_neg_xcms  \\
    prefilter_h=$params.value_of_prefilter_quant_neg_xcms \\
    mzCenterFun=$params.mzCenterFun_quant_neg_xcms \\
    integrate=$params.integrate_quant_neg_xcms \\
    fitgauss=$params.fitgauss_quant_neg_xcms  \\
    methodXset=$params.ipo_methodXset_neg \\
    methodRT=$params.ipo_methodRT_neg \\
    noise_l=$params.ipo_noise_l_neg  \\
    noise_h=$params.ipo_noise_h_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_neg  \\
    snthresh_l=$params.ipo_snthresh_l_neg \\
    snthresh_h=$params.ipo_snthresh_h_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_neg  \\
    integrate=$params.ipo_integrate_neg \\
    fitgauss=$params.ipo_fitgauss_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_neg  \\
    ipo_inv=$ipo_neg_localQ \\
    $filter_argument
"""
NextFlow From line 3200 of master/main.nf 
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"""
nextFlowDIR=\$PWD
xcmsCollect.r input=$inputs_aggregated output=collection_neg.rdata
"""
NextFlow From line 3267 of master/main.nf 
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"""
retCor.r \\
    input=\$PWD/$rdata_files \\
    output=RTcorrected_neg.rdata \\
    method=obiwarp \\
    response_l=$params.ipo_response_l_neg \\
    response_h=$params.ipo_response_h_neg \\
    distFunc=$params.ipo_distFunc_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_neg \\
    factorGap_l=$params.ipo_factorGap_l_neg  \\
    factorGap_h=$params.ipo_factorGap_h_neg \\
    localAlignment=$params.ipo_localAlignment_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_neg \\
    bw_l=$params.ipo_bw_l_neg \\
    bw_h=$params.ipo_bw_h_neg \\
    minfrac_l=$params.ipo_minfrac_l_neg  \\
    minfrac_h=$params.ipo_minfrac_h_neg \\
    mzwid_l=$params.ipo_mzwid_l_neg \\
    mzwid_h=$params.ipo_mzwid_h_neg \\
    minsamp_l=$params.ipo_minsamp_l_neg  \\
    minsamp_h=$params.ipo_minsamp_h_neg \\
    max_l=$params.ipo_max_l_neg \\
    max_h=$params.ipo_max_h_neg \\
    ipo_inv=$ipo_neg_localRT \\
    ncores=$params.ipo_ncores_neg  \\
    profStep=$params.profStep_align_N1_neg_xcms \\
    center=$params.center_align_N1_neg_xcms \\
    response=$params.response_align_N1_neg_xcms  \\
    distFunc=$params.distFunc_align_N1_neg_xcms \\
    gapInit=$params.gapInit_align_N1_neg_xcms \\
    gapExtend=$params.gapExtend_align_N1_neg_xcms  \\
    factorDiag=$params.factorDiag_align_N1_neg_xcms \\
    factorGap=$params.factorGap_align_N1_neg_xcms \\
    localAlignment=$params.localAlignment_align_N1_neg_xcms \\
    $filter_argument \\
    inputraw=$inputs_aggregated
"""
NextFlow From line 3294 of master/main.nf 
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"""
group.r \\
    input=$rdata_files \\
    output=groupN1_neg.rdata \\
    bandwidth=$params.bandwidth_group_N1_neg_xcms \\
    minfrac=$params.minfrac_group_N1_neg_xcms \\
    minsamp=$params.minsamp_group_N1_neg_xcms \\
    max=$params.max_group_N1_neg_xcms  \\
    mzwid=$params.mzwid_group_N1_neg_xcms
"""
NextFlow From line 3354 of master/main.nf 
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"""
blankfilter.r \\
    input=$rdata_files \\
    output=blankFiltered_neg.rdata \\
    method=$params.method_blankfilter_neg_xcms \\
    blank=$params.blank_blankfilter_neg_xcms \\
    sample=$params.sample_blankfilter_neg_xcms \\
    rest=$params.rest_blankfilter_neg_xcms
"""
NextFlow From line 3386 of master/main.nf 
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"""
dilutionfilter.r \\
    input=$rdata_files \\
    output=dilutionFiltered_neg.rdata \\
    Corto=$params.corto_dilutionfilter_neg_xcms  \\
    dilution=$params.dilution_dilutionfilter_neg_xcms \\
    pvalue=$params.pvalue_dilutionfilter_neg_xcms \\
    corcut=$params.corcut_dilutionfilter_neg_xcms \\
    abs=$params.abs_dilutionfilter_neg_xcms
"""
NextFlow From line 3419 of master/main.nf 
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"""
cvfilter.r \\
    input=$rdata_files \\
    output=cvFiltered_neg.rdata \\
    qc=$params.qc_cvfilter_neg_xcms \\
    cvcut=$params.cvcut_cvfilter_neg_xcms
"""
NextFlow From line 3452 of master/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=CameraAnnotatePeaks_neg.rdata
"""
NextFlow From line 3481 of master/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=CameraGroup_neg.rdata \\
    sigma=$params.sigma_group_neg_camera \\
    perfwhm=$params.perfwhm_group_neg_camera \\
    intval=$params.intval_group_neg_camera
"""
NextFlow From line 3502 of master/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=CameraFindAdducts_neg.rdata \\
    ppm=$params.ppm_findaddcuts_neg_camera \\
    polarity=$params.polarity_findaddcuts_neg_camera
"""
NextFlow From line 3528 of master/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=CameraFindIsotopes_neg.rdata \\
    maxcharge=$params.maxcharge_findisotopes_neg_camera
"""
NextFlow From line 3553 of master/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 3584 of master/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$input_args \\
    output=MapMsms2Camera_neg.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_neg_msnbase \\
    rt=$params.rt_mapmsmstocamera_neg_msnbase
"""
NextFlow From line 3611 of master/main.nf 
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"""
mkdir out

MS2ToMetFrag.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=out \\
    precursorppm=$params.precursorppm_msmstoparam_neg_msnbase  \\
    fragmentppm=$params.fragmentppm_msmstoparam_neg_msnbase \\
    fragmentabs=$params.fragmentabs_msmstoparam_neg_msnbase \\
    database=$params.database_msmstoparam_neg_msnbase  \\
    mode=$params.mode_msmstoparam_neg_msnbase \\
    adductRules=$params.adductRules_msmstoparam_neg_msnbase \\
    minPeaks=$params.minPeaks_msmstoparam_neg_msnbase

ls out/ -A -1  | cut -d'_' -f4- | tr ' ' '\n' | sort -u | xargs -I %  find out/ -type f -iname *% -exec zip %.zip {} +
"""
NextFlow From line 3638 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}_class_Csifingerid_neg.csv

fingerID.r \\
    input=\$PWD/inputs \\
    database=$params.database_csifingerid_neg_csifingerid \\
    tryOffline=T \\
    output=\$PWD/outputs/ \\
    ncores=$params.ncore_csifingerid_neg_csifingerid  \\
    timeout=$params.timeout_csifingerid_neg_csifingerid \\
    canopus=T \\
    canopusOutput=\$PWD/${parameters.baseName}_class_Csifingerid_neg.csv

zip -j -r ${parameters.baseName}_Csifingerid_neg.zip outputs/*.csv
"""
NextFlow From line 3682 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r Csifingerid_neg.zip all

aggregateMetfrag.r \\
    inputs=Csifingerid_neg.zip \\
    realNames=Csifingerid_neg.zip \\
    output=aggregated_identification_csifingerid_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_csifingerid_neg.csv
"""
NextFlow From line 3717 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_csifingerid_neg.csv \\
        readTable=T
else
    touch pep_identification_csifingerid_neg.csv
fi
"""
NextFlow From line 3751 of master/main.nf 
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"""
if [ -s $csifingerid_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$csifingerid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera  \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_csifingerid.txt  \\
        outputVariables=varsNEGout_neg_csifingerid.txt \\
        outputMetaData=metadataNEGout_neg_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera  \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_csifingerid.txt \\
        outputVariables=varsNEGout_neg_csifingerid.txt  \\
        outputMetaData=metadataNEGout_neg_csifingerid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 3782 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv
find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_neg_metfrag \\
        run_metfrag.sh  \\
        -p {} \\
        -f \$PWD/outputs/{/.}.csv \\
        -l "\$PWD/$metfrag_database" \\
        -s "OfflineMetFusionScore"
zip -j -r ${parameters.baseName}_metfrag_neg.zip outputs/*.csv
"""
NextFlow From line 3878 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r metfrag_neg.zip all

aggregateMetfrag.r \\
    inputs=metfrag_neg.zip \\
    realNames=metfrag_neg.zip \\
    output=aggregated_identification_metfrag_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_metfrag_neg.csv
"""
NextFlow From line 3911 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=FragmenterScore \\
        output=pep_identification_metfrag_neg.csv \\
        readTable=T
else
    touch pep_identification_metfrag_neg.csv
fi
"""
NextFlow From line 3943 of master/main.nf 
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"""
if [ -s $metfrag_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$metfrag_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera  \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_metfrag.txt  \\
        outputVariables=varsNEGout_neg_metfrag.txt \\
        outputMetaData=metadataNEGout_neg_metfrag.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=FragmenterScore  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera  \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_metfrag.txt \\
        outputVariables=varsNEGout_neg_metfrag.txt \\
        outputMetaData=metadataNEGout_neg_metfrag.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 3975 of master/main.nf 
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"""
mkdir inputs
mkdir outputs
unzip  -j $parameters -d inputs/
touch ${parameters.baseName}.csv

find "\$PWD/inputs" -type f | \\
    parallel \\
        -j $params.ncore_neg_cfmid \\
        cfmid.r \\
        input={} \\
        realName={/} \\
        databaseFile=\$PWD/$cfmid_database \\
        output=\$PWD/outputs/{/.}.csv \\
        candidate_id=$params.candidate_id_identification_neg_cfmid \\
        candidate_inchi_smiles=$params.candidate_inchi_smiles_identification_neg_cfmid  \\
        candidate_mass=$params.candidate_mass_identification_neg_cfmid \\
        databaseNameColumn=$params.database_name_column_identification_neg_cfmid \\
        databaseInChIColumn=$params.database_inchI_column_identification_neg_cfmid \\
        scoreType=Jaccard

zip -j -r ${parameters.baseName}_cfmid_neg.zip outputs/*.csv
"""
NextFlow From line 4060 of master/main.nf 
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"""
ulimit -s unlimited
mkdir all
for x in *.zip ; do unzip -d all -o -u \$x ; done
zip -r cfmid_neg.zip all

aggregateMetfrag.r \\
    inputs=cfmid_neg.zip \\
    realNames=cfmid_neg.zip \\
    output=aggregated_identification_cfmid_neg.csv \\
    filetype=zip \\
    outTable=T

sed -i '/^\$/d' aggregated_identification_cfmid_neg.csv
"""
NextFlow From line 4101 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=Jaccard_Score \\
        output=pep_identification_cfmid_neg.csv \\
        readTable=T
else
    touch pep_identification_cfmid_neg.csv
fi
"""
NextFlow From line 4134 of master/main.nf 
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"""
if [ -s $cfmid_input_identification ]; then
    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$cfmid_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera  \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_cfmid.txt  \\
        outputVariables=varsNEGout_neg_cfmid.txt \\
        outputMetaData=metadataNEGout_neg_cfmid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=Jaccard_Score  \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera  \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera  \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_cfmid.txt \\
        outputVariables=varsNEGout_neg_cfmid.txt \\
        outputMetaData=metadataNEGout_neg_cfmid.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 4166 of master/main.nf 
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"""
PeakPickerHiRes -in $mzMLFile -out $mzMLFile -ini $setting_file
"""
NextFlow From line 4244 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 4267 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 4288 of master/main.nf 
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"""
touch quant_params_library_neg.json
touch rt_params_library_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    response_l=$params.ipo_response_l_library_neg \\
    response_h=$params.ipo_response_h_library_neg \\
    distFunc=$params.ipo_distFunc_library_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_library_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_library_neg \\
    factorGap_l=$params.ipo_factorGap_l_library_neg  \\
    factorGap_h=$params.ipo_factorGap_h_library_neg \\
    localAlignment=$params.ipo_localAlignment_library_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_library_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_library_neg \\
    bw_l=$params.ipo_bw_l_library_neg \\
    bw_h=$params.ipo_bw_h_library_neg \\
    minfrac_l=$params.ipo_minfrac_l_library_neg  \\
    minfrac_h=$params.ipo_minfrac_h_library_neg \\
    mzwid_l=$params.ipo_mzwid_l_library_neg \\
    mzwid_h=$params.ipo_mzwid_h_library_neg \\
    minsamp_l=$params.ipo_minsamp_l_library_neg  \\
    minsamp_h=$params.ipo_minsamp_h_library_neg \\
    max_l=$params.ipo_max_l_library_neg \\
    max_h=$params.ipo_max_h_library_neg \\
    ncores=$params.ipo_ncores_library_neg \\
    outputxset=quant_params_library_neg.json \\
    outputrt=rt_params_library_neg.json
"""
NextFlow IPO From line 4322 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_neg_xcms \\
    noise=$params.noise_quant_library_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_neg_xcms  \\
    mzdiff=$params.mzdiff_quant_library_neg_xcms \\
    snthresh=$params.snthresh_quant_library_neg_xcms \\
    prefilter_l=$params.prefilter_quant_library_neg_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_neg_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_neg_xcms \\
    integrate=$params.integrate_quant_library_neg_xcms \\
    fitgauss=$params.fitgauss_quant_library_neg_xcms  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    ipo_inv=$ipo_library_neg_localQ \\
    $filter_argument
"""
NextFlow From line 4401 of master/main.nf 
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"""
FeatureFinderMetabo -in $mzMLFile -out ${mzMLFile.baseName}.featureXML -ini $setting_file
"""
NextFlow From line 4467 of master/main.nf 
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"""
featurexmlToCamera.r \\
    input=$mzMLFile \\
    realFileName=$mzMLFile \\
    mzMLfiles=\$PWD/$mzMLFile2 \\
    polarity=negative \\
    output=${mzMLFile.baseName}.rdata \\
    sampleClass=library \\
    changeNameTO=${mzMLFile.baseName}.mzML
"""
NextFlow From line 4488 of master/main.nf 
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"""
touch quant_params_library_neg.json
touch rt_params_library_neg.json

ipo.r \\
    input=$inputs_aggregated \\
    quantOnly=TRUE \\
    allSamples=TRUE  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    response_l=$params.ipo_response_l_library_neg \\
    response_h=$params.ipo_response_h_library_neg \\
    distFunc=$params.ipo_distFunc_library_neg \\
    factorDiag_l=$params.ipo_factorDiag_l_library_neg \\
    factorDiag_h=$params.ipo_factorDiag_h_library_neg \\
    factorGap_l=$params.ipo_factorGap_l_library_neg  \\
    factorGap_h=$params.ipo_factorGap_h_library_neg \\
    localAlignment=$params.ipo_localAlignment_library_neg \\
    ipo_gapInit_l=$params.ipo_gapInit_l_library_neg \\
    ipo_gapInit_h=$params.ipo_gapInit_h_library_neg \\
    ipo_gapExtend_l=$params.ipo_gapExtend_l_library_neg  \\
    ipo_gapExtend_h=$params.ipo_gapExtend_h_library_neg \\
    ipo_profStep_l=$params.ipo_profStep_l_library_neg \\
    ipo_profStep_h=$params.ipo_profStep_h_library_neg \\
    bw_l=$params.ipo_bw_l_library_neg \\
    bw_h=$params.ipo_bw_h_library_neg \\
    minfrac_l=$params.ipo_minfrac_l_library_neg  \\
    minfrac_h=$params.ipo_minfrac_h_library_neg \\
    mzwid_l=$params.ipo_mzwid_l_library_neg \\
    mzwid_h=$params.ipo_mzwid_h_library_neg \\
    minsamp_l=$params.ipo_minsamp_l_library_neg  \\
    minsamp_h=$params.ipo_minsamp_h_library_neg \\
    max_l=$params.ipo_max_l_library_neg \\
    max_h=$params.ipo_max_h_library_neg \\
    ncores=$params.ipo_ncores_library_neg \\
    outputxset=quant_params_library_neg.json \\
    outputrt=rt_params_library_neg.json
"""
NextFlow IPO From line 4521 of master/main.nf 
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"""
findPeaks.r \\
    input=\$PWD/$mzMLFile \\
    output=\$PWD/${mzMLFile.baseName}.rdata \\
    ppm=$params.masstrace_ppm_library_neg_xcms \\
    peakwidthLow=$params.peakwidthlow_quant_library_neg_xcms  \\
    peakwidthHigh=$params.peakwidthhigh_quant_library_neg_xcms \\
    noise=$params.noise_quant_library_neg_xcms \\
    polarity=negative \\
    realFileName=$mzMLFile \\
    sampleClass=$params.sampleclass_quant_library_neg_xcms  \\
    mzdiff=$params.mzdiff_quant_library_neg_xcms \\
    snthresh=$params.snthresh_quant_library_neg_xcms \\
    prefilter_l=$params.prefilter_quant_library_neg_xcms \\
    prefilter_h=$params.value_of_prefilter_quant_library_neg_xcms  \\
    mzCenterFun=$params.mzCenterFun_quant_library_neg_xcms \\
    integrate=$params.integrate_quant_library_neg_xcms \\
    fitgauss=$params.fitgauss_quant_library_neg_xcms  \\
    methodXset=$params.ipo_methodXset_library_neg \\
    methodRT=$params.ipo_methodRT_library_neg \\
    noise_l=$params.ipo_noise_l_library_neg  \\
    noise_h=$params.ipo_noise_h_library_neg \\
    prefilter_l_l=$params.ipo_prefilter_l_l_library_neg \\
    prefilter_l_h=$params.ipo_prefilter_l_h_library_neg  \\
    prefilter_h_l=$params.ipo_prefilter_h_l_library_neg \\
    prefilter_h_h=$params.ipo_prefilter_h_h_library_neg  \\
    snthresh_l=$params.ipo_snthresh_l_library_neg \\
    snthresh_h=$params.ipo_snthresh_h_library_neg \\
    mzCenterFun=$params.ipo_mzCenterFun_library_neg  \\
    integrate=$params.ipo_integrate_library_neg \\
    fitgauss=$params.ipo_fitgauss_library_neg \\
    ipo_min_peakwidth_l=$params.ipo_min_peakwidth_l_library_neg  \\
    ipo_min_peakwidth_h=$params.ipo_min_peakwidth_h_library_neg \\
    ipo_max_peakwidth_l=$params.ipo_max_peakwidth_l_library_neg \\
    ipo_max_peakwidth_h=$params.ipo_max_peakwidth_h_library_neg \\
    ipo_ppm_l=$params.ipo_ppm_l_library_neg  \\
    ipo_ppm_h=$params.ipo_ppm_h_library_neg \\
    ipo_mzdiff_l=$params.ipo_mzdiff_l_library_neg \\
    ipo_mzdiff_h=$params.ipo_mzdiff_h_library_neg \\
    ipo_charge_camera=$params.ipo_charge_camera_library_neg  \\
    ipo_max_ppm_camera=$params.ipo_max_ppm_camera_library_neg  \\
    ipo_inv=$ipo_library_neg_localQ \\
    $filter_argument
"""
NextFlow From line 4600 of master/main.nf 
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"""
xsAnnotate.r input=$rdata_files output=${rdata_files.baseName}.rdata
"""
NextFlow From line 4664 of master/main.nf 
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"""
groupFWHM.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    sigma=$params.sigma_group_library_neg_camera \\
    perfwhm=$params.perfwhm_group_library_neg_camera \\
    intval=$params.intval_group_library_neg_camera
"""
NextFlow From line 4685 of master/main.nf 
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"""
findAdducts.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    ppm=$params.ppm_findaddcuts_library_neg_camera \\
    polarity=$params.polarity_findaddcuts_library_neg_camera
"""
NextFlow From line 4711 of master/main.nf 
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"""
findIsotopes.r \\
    input=$rdata_files \\
    output=${rdata_files.baseName}.rdata \\
    maxcharge=$params.maxcharge_findisotopes_library_neg_camera
"""
NextFlow From line 4737 of master/main.nf 
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"""
readMS2MSnBase.r \\
    input=$mzMLFile \\
    output=${mzMLFile.baseName}_ReadMsmsLibrary.rdata \\
    inputname=${mzMLFile.baseName}
"""
NextFlow From line 4761 of master/main.nf 
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"""
mapMS2ToCamera.r \\
    inputCAMERA=$rdata_files_ms1 \\
    inputMS2=$rdata_files_ms2 \\
    output=${rdata_files_ms1.baseName}_MapMsms2Camera_library_neg.rdata  \\
    ppm=$params.ppm_mapmsmstocamera_library_neg_msnbase \\
    rt=$params.rt_mapmsmstocamera_library_neg_msnbase
"""
NextFlow From line 4790 of master/main.nf 
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"""
mkdir out
createLibrary.r \\
    inputCAMERA=$rdata_camera \\
    precursorppm=$params.ppm_create_library_neg_msnbase \\
    inputMS2=$ms2_data \\
    output=${rdata_camera.baseName}.csv  \\
    inputLibrary=$library_desc \\
    rawFileName=$params.raw_file_name_preparelibrary_neg_msnbase \\
    compundID=$params.compund_id_preparelibrary_neg_msnbase  \\
    compoundName=$params.compound_name_preparelibrary_neg_msnbase \\
    mzCol=$params.mz_col_preparelibrary_neg_msnbase \\
    whichmz=$params.which_mz_preparelibrary_neg_msnbase
"""
NextFlow From line 4822 of master/main.nf 
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"""
collectLibrary.r \\
    inputs=$aggregatecdlibrary \\
    realNames=$aggregatecdlibrary \\
    output=library_neg.csv
"""
NextFlow From line 4855 of master/main.nf 
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"""
#!env Rscript
Files<-list.files(,pattern = "zip",full.names=T)
Files_org<-list.files(,pattern = "zip")
for(f in Files){
    zip::unzip(zipfile = f,junkpaths = T)
}
Files<-list.files(,pattern = "txt",full.names=T)
FilesTMP<-sapply(strsplit(split = "_",fixed = T,x = basename(Files)),function(x){paste(x[-1],collapse = "_")})
FileDub<-Files[duplicated(FilesTMP)]
for(x in FileDub){
    file.remove(x)
}
files_to_pass<-list.files(pattern="txt")
files_to_pass<-files_to_pass[!files_to_pass%in%Files_org]
zip::zip(zipfile="mappedtometfrag_neg.zip",files=files_to_pass)
"""
NextFlow From line 4879 of master/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters  \\
    -out aggregated_identification_library_neg.csv \\
    -th "-1" \\
    -im neg  \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_neg_msnbase
sed -i '/^\$/d' aggregated_identification_library_neg.csv
"""
NextFlow From line 4918 of master/main.nf 
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"""
librarySearchEngine.r \\
    -l $libraryFile \\
    -i $parameters \\
    -out aggregated_identification_library_neg.csv \\
    -th "-1" \\
    -im neg \\
    -ts Scoredotproduct \\
    -rs 1000 \\
    -ncore $params.ncore_searchengine_library_neg_msnbase
sed -i '/^\$/d' aggregated_identification_library_neg.csv
"""
NextFlow From line 4950 of master/main.nf 
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"""
if [ -s $identification_result ]; then
    metfragPEP.r \\
        input=$identification_result \\
        score=score \\
        output=pep_identification_library_neg.csv \\
        readTable=T
else
    touch pep_identification_library_neg.csv
fi
"""
NextFlow From line 4981 of master/main.nf 
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"""
if [ -s $library_input_identification ]; then

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputscores=$library_input_identification \\
        inputpheno=$phenotype_file \\
        ppm=$params.ppm_output_neg_camera  \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera \\
        selectedType=$params.selected_type_output_neg_camera  \\
        rename=$params.rename_output_neg_camera \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
        combineReplicate=$params.combine_replicate_output_neg_camera  \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_library.txt  \\
        outputVariables=varsNEGout_neg_library.txt \\
        outputMetaData=metadataNEGout_neg_library.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

else

    prepareOutput.r \\
        inputcamera=$camera_input_quant \\
        inputpheno=$phenotype_file  \\
        ppm=$params.ppm_output_neg_camera \\
        rt=$params.rt_output_neg_camera \\
        higherTheBetter=true  \\
        scoreColumn=score \\
        impute=$params.impute_output_neg_camera \\
        typeColumn=$params.type_column_output_neg_camera  \\
        selectedType=$params.selected_type_output_neg_camera \\
        rename=$params.rename_output_neg_camera  \\
        renameCol=$params.rename_col_output_neg_camera \\
        onlyReportWithID=$params.only_report_with_id_output_neg_camera  \\
        combineReplicate=$params.combine_replicate_output_neg_camera \\
        combineReplicateColumn=$params.combine_replicate_column_output_neg_camera  \\
        log=$params.log_output_neg_camera \\
        sampleCoverage=$params.sample_coverage_output_neg_camera \\
        outputPeakTable=peaktableNEGout_neg_library.txt  \\
        outputVariables=varsNEGout_neg_library.txt \\
        outputMetaData=metadataNEGout_neg_library.txt \\
        Ifnormalize=$params.normalize_output_neg_camera

fi
"""
NextFlow From line 5014 of master/main.nf 
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"""
prepareOutput.r \\
    inputcamera=$camera_input_quant \\
    inputpheno=$phenotype_file \\
    ppm=$params.ppm_output_neg_camera \\
    rt=$params.rt_output_neg_camera \\
    higherTheBetter=true \\
    scoreColumn=score  \\
    impute=$params.impute_output_neg_camera \\
    typeColumn=$params.type_column_output_neg_camera \\
    selectedType=$params.selected_type_output_neg_camera \\
    rename=$params.rename_output_neg_camera  \\
    renameCol=$params.rename_col_output_neg_camera \\
    onlyReportWithID=$params.only_report_with_id_output_neg_camera \\
    combineReplicate=$params.combine_replicate_output_neg_camera  \\
    combineReplicateColumn=$params.combine_replicate_column_output_neg_camera \\
    log=$params.log_output_neg_camera \\
    sampleCoverage=$params.sample_coverage_output_neg_camera  \\
    outputPeakTable=peaktableNEGout_NEG_noid.txt \\
    outputVariables=varsNEGout_neg_noid.txt \\
    outputMetaData=metadataNEGout_neg_noid.txt \\
    Ifnormalize=$params.normalize_output_neg_camera
"""
NextFlow From line 5086 of master/main.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://nf-co.re/metaboigniter
Name: metaboigniter
Version: 1.0.1
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