Protein Conformational Ensemble Generation and Analysis Workflow using ELIXIR 3D-Bioinfo and PDBe-KB

public public 1yr ago Version: Version 2 0 bookmarks
View Workflow
Report
cwl-protein-conformational-ensembles-generation
cwl-protein-conformational-ensembles-generation
cwl-protein-conformational-ensembles-generation
View Workflow

Protein Conformational ensembles generation

Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:

Building on PDBe-KB to chart and characterize the conformation landscape of native proteins

This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility , step by step, using the BioExcel Building Blocks library (biobb) .

Conformational landscape of native proteins

Proteins are dynamic systems that adopt multiple conformational states , a property essential for many biological processes (e.g. binding other proteins, nucleic acids, small molecule ligands, or switching between functionaly active and inactive states). Characterizing the different conformational states of proteins and the transitions between them is therefore critical for gaining insight into their biological function and can help explain the effects of genetic variants in health and disease and the action of drugs.

Structural biology has become increasingly efficient in sampling the different conformational states of proteins. The PDB has currently archived more than 170,000 individual structures , but over two thirds of these structures represent multiple conformations of the same or related protein, observed in different crystal forms, when interacting with other proteins or other macromolecules, or upon binding small molecule ligands. Charting this conformational diversity across the PDB can therefore be employed to build a useful approximation of the conformational landscape of native proteins.

A number of resources and tools describing and characterizing various often complementary aspects of protein conformational diversity in known structures have been developed, notably by groups in Europe. These tools include algorithms with varying degree of sophistication, for aligning the 3D structures of individual protein chains or domains, of protein assemblies, and evaluating their degree of structural similarity . Using such tools one can align structures pairwise , compute the corresponding similarity matrix , and identify ensembles of structures/conformations with a defined similarity level that tend to recur in different PDB entries, an operation typically performed using clustering methods. Such workflows are at the basis of resources such as CATH, Contemplate, or PDBflex that offer access to conformational ensembles comprised of similar conformations clustered according to various criteria. Other types of tools focus on differences between protein conformations , identifying regions of proteins that undergo large collective displacements in different PDB entries, those that act as hinges or linkers , or regions that are inherently flexible .

To build a meaningful approximation of the conformational landscape of native proteins, the conformational ensembles (and the differences between them), identified on the basis of structural similarity/dissimilarity measures alone, need to be biophysically characterized . This may be approached at two different levels .

  • At the biological level , it is important to link observed conformational ensembles , to their functional roles by evaluating the correspondence with protein family classifications based on sequence information and functional annotations in public databases e.g. Uniprot, PDKe-Knowledge Base (KB). These links should provide valuable mechanistic insights into how the conformational and dynamic properties of proteins are exploited by evolution to regulate their biological function .

  • At the physical level one needs to introduce energetic consideration to evaluate the likelihood that the identified conformational ensembles represent conformational states that the protein (or domain under study) samples in isolation. Such evaluation is notoriously challenging and can only be roughly approximated by using computational methods to evaluate the extent to which the observed conformational ensembles can be reproduced by algorithms that simulate the dynamic behavior of protein systems. These algorithms include the computationally expensive classical molecular dynamics (MD) simulations to sample local thermal fluctuations but also faster more approximate methods such as Elastic Network Models and Normal Node Analysis (NMA) to model low energy collective motions . Alternatively, enhanced sampling molecular dynamics can be used to model complex types of conformational changes but at a very high computational cost.

The ELIXIR 3D-Bioinfo Implementation Study Building on PDBe-KB to chart and characterize the conformation landscape of native proteins focuses on:

  1. Mapping the conformational diversity of proteins and their homologs across the PDB.
  2. Characterize the different flexibility properties of protein regions, and link this information to sequence and functional annotation.
  3. Benchmark computational methods that can predict a biophysical description of protein motions.

Code Snippets

11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
baseCommand: bd_run

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/flexserv/structure.ca.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_log_path:
    label: Output log file
    doc: |-
      Output log file
      Type: string
      File type: output
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/bd_run_out.log
    type: string
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --output_log_path
    default: system.log

  output_crd_path:
    label: Output ensemble
    doc: |-
      Output ensemble
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/bd_run_out.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 3
      prefix: --output_crd_path
    default: system.crd

  config:
    label: Advanced configuration options for biobb_flexserv BDRun
    doc: |-
      Advanced configuration options for biobb_flexserv BDRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv BDRun documentation: https://biobb-flexserv.readthedocs.io/en/latest/flexserv.html#module-flexserv.bd_run
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/bd_run.cwl 
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
baseCommand: concoord_disco

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input structure file in PDB format
    doc: |-
      Input structure file in PDB format
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  input_dat_path:
    label: Input dat with structure interpretation and bond definitions
    doc: |-
      Input dat with structure interpretation and bond definitions
      Type: string
      File type: input
      Accepted formats: dat, txt
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/dist.dat
    type: File
    format:
    - edam:format_1637
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --input_dat_path

  output_traj_path:
    label: Output trajectory file
    doc: |-
      Output trajectory file
      Type: string
      File type: output
      Accepted formats: pdb, xtc, gro
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_trj.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_3875
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_traj_path
    default: system.pdb

  output_rmsd_path:
    label: Output rmsd file
    doc: |-
      Output rmsd file
      Type: string
      File type: output
      Accepted formats: dat
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_rmsd.dat
    type: string
    format:
    - edam:format_1637
    inputBinding:
      position: 4
      prefix: --output_rmsd_path
    default: system.dat

  output_bfactor_path:
    label: Output B-factor file
    doc: |-
      Output B-factor file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_bfactor.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 5
      prefix: --output_bfactor_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_flexdyn ConcoordDisco
    doc: |-
      Advanced configuration options for biobb_flexdyn ConcoordDisco. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn ConcoordDisco documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.concoord_disco
    type: string?
    inputBinding:
      prefix: --config
CWL concoord From line 11 of biobb_adapters/concoord_disco.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
baseCommand: concoord_dist

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Input structure file
    doc: |-
      Input structure file
      Type: string
      File type: input
      Accepted formats: pdb, gro
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_2033
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_pdb_path:
    label: Output pdb file
    doc: |-
      Output pdb file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  output_gro_path:
    label: Output gro file
    doc: |-
      Output gro file
      Type: string
      File type: output
      Accepted formats: gro
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.gro
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_gro_path
    default: system.gro

  output_dat_path:
    label: Output dat with structure interpretation and bond definitions
    doc: |-
      Output dat with structure interpretation and bond definitions
      Type: string
      File type: output
      Accepted formats: dat, txt
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2330
    inputBinding:
      position: 4
      prefix: --output_dat_path
    default: system.dat

  config:
    label: Advanced configuration options for biobb_flexdyn ConcoordDist
    doc: |-
      Advanced configuration options for biobb_flexdyn ConcoordDist. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn ConcoordDist documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.concoord_dist
    type: string?
    inputBinding:
      prefix: --config
CWL concoord From line 11 of biobb_adapters/concoord_dist.cwl 
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
baseCommand: cpptraj_convert

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output processed trajectory
    doc: |-
      Path to the output processed trajectory
      Type: string
      File type: output
      Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.convert.netcdf
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_2033
    - edam:format_3878
    - edam:format_1476
    - edam:format_3816
    - edam:format_3885
    - edam:format_3910
    - edam:format_3875
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.mdcrd

  config:
    label: Advanced configuration options for biobb_analysis CpptrajConvert
    doc: |-
      Advanced configuration options for biobb_analysis CpptrajConvert. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis CpptrajConvert documentation: https://biobb-analysis.readthedocs.io/en/latest/ambertools.html#module-ambertools.cpptraj_convert
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis CPPTRAJ From line 12 of biobb_adapters/cpptraj_convert.cwl 
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
baseCommand: cpptraj_mask

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output processed trajectory
    doc: |-
      Path to the output processed trajectory
      Type: string
      File type: output
      Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.mask.netcdf
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_2033
    - edam:format_3878
    - edam:format_1476
    - edam:format_3816
    - edam:format_3885
    - edam:format_3910
    - edam:format_3875
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.mdcrd

  config:
    label: Advanced configuration options for biobb_analysis CpptrajMask
    doc: |-
      Advanced configuration options for biobb_analysis CpptrajMask. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis CpptrajMask documentation: https://biobb-analysis.readthedocs.io/en/latest/ambertools.html#module-ambertools.cpptraj_mask
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis CPPTRAJ From line 12 of biobb_adapters/cpptraj_mask.cwl 
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
baseCommand: cpptraj_rms

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_top_path:
    label: Path to the input structure or topology file
    doc: |-
      Path to the input structure or topology file
      Type: string
      File type: input
      Accepted formats: top, pdb, prmtop, parmtop, zip
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top
    type: File
    format:
    - edam:format_3881
    - edam:format_1476
    - edam:format_3881
    - edam:format_3881
    - edam:format_3987
    inputBinding:
      position: 1
      prefix: --input_top_path

  input_traj_path:
    label: Path to the input trajectory to be processed
    doc: |-
      Path to the input trajectory to be processed
      Type: string
      File type: input
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_cpptraj_path:
    label: Path to the output processed analysis
    doc: |-
      Path to the output processed analysis
      Type: string
      File type: output
      Accepted formats: dat, agr, xmgr, gnu
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2033
    - edam:format_2033
    - edam:format_2033
    inputBinding:
      position: 3
      prefix: --output_cpptraj_path
    default: system.dat

  input_exp_path:
    label: Path to the experimental reference file (required if reference = experimental)
    doc: |-
      Path to the experimental reference file (required if reference = experimental)
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb
    type: File?
    format:
    - edam:format_1476
    inputBinding:
      prefix: --input_exp_path

  output_traj_path:
    label: Path to the output processed trajectory
    doc: |-
      Path to the output processed trajectory
      Type: string
      File type: output
      Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3650
    - edam:format_3650
    - edam:format_3650
    - edam:format_3886
    - edam:format_3886
    - edam:format_3886
    - edam:format_3878
    - edam:format_3887
    - edam:format_2033
    - edam:format_1476
    - edam:format_3816
    - edam:format_3910
    - edam:format_2033
    - edam:format_3885
    - edam:format_3875
    - edam:format_1477
    - edam:format_2333
    - edam:format_2033
    - edam:format_3814
    - edam:format_2033
    inputBinding:
      prefix: --output_traj_path
    default: system.mdcrd

  config:
    label: Advanced configuration options for biobb_analysis CpptrajRms
    doc: |-
      Advanced configuration options for biobb_analysis CpptrajRms. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis CpptrajRms documentation: https://biobb-analysis.readthedocs.io/en/latest/ambertools.html#module-ambertools.cpptraj_rms
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis CPPTRAJ From line 12 of biobb_adapters/cpptraj_rms.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
baseCommand: dmd_run

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/flexserv/structure.ca.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_log_path:
    label: Output log file
    doc: |-
      Output log file
      Type: string
      File type: output
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/dmd_run_out.log
    type: string
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --output_log_path
    default: system.log

  output_crd_path:
    label: Output ensemble
    doc: |-
      Output ensemble
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/dmd_run_out.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 3
      prefix: --output_crd_path
    default: system.crd

  config:
    label: Advanced configuration options for biobb_flexserv DMDRun
    doc: |-
      Advanced configuration options for biobb_flexserv DMDRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv DMDRun documentation: https://biobb-flexserv.readthedocs.io/en/latest/flexserv.html#module-flexserv.dmd_run
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/dmd_run.cwl 
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
baseCommand: extract_chain

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Input structure file path
    doc: |-
      Input structure file path
      Type: string
      File type: input
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_chain.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_structure_path:
    label: Output structure file path
    doc: |-
      Output structure file path
      Type: string
      File type: output
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_chain.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_structure_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_structure_utils ExtractAtoms
    doc: |-
      Advanced configuration options for biobb_structure_utils ExtractAtoms. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractAtoms documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_chain
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_structure_utils From line 12 of biobb_adapters/extract_chain.cwl 
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
baseCommand: extract_model

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_structure_utils:4.0.0--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Input structure file path
    doc: |-
      Input structure file path
      Type: string
      File type: input
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/extract_model.pdb
    type: File
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_structure_path:
    label: Output structure file path
    doc: |-
      Output structure file path
      Type: string
      File type: output
      Accepted formats: pdb, pdbqt
      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_extract_model.pdb
    type: string
    format:
    - edam:format_1476
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_structure_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_structure_utils ExtractModel
    doc: |-
      Advanced configuration options for biobb_structure_utils ExtractModel. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_structure_utils ExtractModel documentation: https://biobb-structure-utils.readthedocs.io/en/latest/utils.html#module-utils.extract_model
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_structure_utils From line 12 of biobb_adapters/extract_model.cwl 
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
baseCommand: gmx_cluster

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_0

inputs:
  input_structure_path:
    label: Path to the input structure file
    doc: |-
      Path to the input structure file
      Type: string
      File type: input
      Accepted formats: tpr, gro, g96, pdb, brk, ent
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr
    type: File
    format:
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_2033
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_structure_path

  input_traj_path:
    label: Path to the GROMACS trajectory file
    doc: |-
      Path to the GROMACS trajectory file
      Type: string
      File type: input
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr
    type: File
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    - edam:format_3878
    inputBinding:
      position: 2
      prefix: --input_traj_path

  output_pdb_path:
    label: Path to the output cluster file
    doc: |-
      Path to the output cluster file
      Type: string
      File type: output
      Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_cluster.pdb
    type: string
    format:
    - edam:format_3875
    - edam:format_3910
    - edam:format_2333
    - edam:format_2033
    - edam:format_2033
    - edam:format_1476
    - edam:format_3876
    inputBinding:
      position: 3
      prefix: --output_pdb_path
    default: system.xtc

  input_index_path:
    label: Path to the GROMACS index file
    doc: |-
      Path to the GROMACS index file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_index_path

  output_cluster_log_path:
    label: Path to the output log file
    doc: |-
      Path to the output log file
      Type: string
      File type: output
      Accepted formats: log
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_cluster.log
    type: string
    format:
    - edam:format_2330
    inputBinding:
      prefix: --output_cluster_log_path
    default: system.log

  output_rmsd_cluster_xpm_path:
    label: Path to the output X PixMap compatible matrix file
    doc: |-
      Path to the output X PixMap compatible matrix file
      Type: string
      File type: output
      Accepted formats: xpm
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_rmsd-clust.xpm
    type: string
    format:
    - edam:format_3599
    inputBinding:
      prefix: --output_rmsd_cluster_xpm_path
    default: system.xpm

  output_rmsd_dist_xvg_path:
    label: Path to xvgr/xmgr file
    doc: |-
      Path to xvgr/xmgr file
      Type: string
      File type: output
      Accepted formats: xvg
      Example file: https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gmx_cluster_rmsd-dist.xvg
    type: string
    format:
    - edam:format_2330
    inputBinding:
      prefix: --output_rmsd_dist_xvg_path
    default: system.xvg

  config:
    label: Advanced configuration options for biobb_analysis GMXCluster
    doc: |-
      Advanced configuration options for biobb_analysis GMXCluster. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_analysis GMXCluster documentation: https://biobb-analysis.readthedocs.io/en/latest/gromacs.html#module-gromacs.gmx_cluster
    type: string?
    inputBinding:
      prefix: --config
CWL biobb_analysis Gromacs From line 12 of biobb_adapters/gmx_cluster.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
baseCommand: imod_imc

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure_cleaned.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  input_dat_path:
    label: Input dat with normal modes
    doc: |-
      Input dat with normal modes
      Type: string
      File type: input
      Accepted formats: dat, txt
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/imod_imode_evecs.dat
    type: File
    format:
    - edam:format_1637
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --input_dat_path

  output_traj_path:
    label: Output multi-model PDB file with the generated ensemble
    doc: |-
      Output multi-model PDB file with the generated ensemble
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imc_output.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 3
      prefix: --output_traj_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_flexdyn imod_imc
    doc: |-
      Advanced configuration options for biobb_flexdyn imod_imc. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn imod_imc documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.imod_imc
    type: string?
    inputBinding:
      prefix: --config
CWL IMOD From line 11 of biobb_adapters/imod_imc.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
baseCommand: imod_imode

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_dat_path:
    label: Output dat with normal modes
    doc: |-
      Output dat with normal modes
      Type: string
      File type: output
      Accepted formats: dat, txt
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imode_evecs.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --output_dat_path
    default: system.dat

  config:
    label: Advanced configuration options for biobb_flexdyn imod_imode
    doc: |-
      Advanced configuration options for biobb_flexdyn imod_imode. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn imod_imode documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.imod_imode
    type: string?
    inputBinding:
      prefix: --config
CWL IMOD From line 11 of biobb_adapters/imod_imode.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
baseCommand: make_ndx

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_gromacs:4.0.0--pyhdfd78af_1

inputs:
  input_structure_path:
    label: Path to the input GRO/PDB/TPR file
    doc: |-
      Path to the input GRO/PDB/TPR file
      Type: string
      File type: input
      Accepted formats: gro, pdb, tpr
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/make_ndx.tpr
    type: File
    format:
    - edam:format_2033
    - edam:format_1476
    - edam:format_2333
    inputBinding:
      position: 1
      prefix: --input_structure_path

  output_ndx_path:
    label: Path to the output index NDX file
    doc: |-
      Path to the output index NDX file
      Type: string
      File type: output
      Accepted formats: ndx
      Example file: https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_make_ndx.ndx
    type: string
    format:
    - edam:format_2033
    inputBinding:
      position: 2
      prefix: --output_ndx_path
    default: system.ndx

  input_ndx_path:
    label: Path to the input index NDX file
    doc: |-
      Path to the input index NDX file
      Type: string
      File type: input
      Accepted formats: ndx
      Example file: null
    type: File?
    format:
    - edam:format_2033
    inputBinding:
      prefix: --input_ndx_path

  config:
    label: Advanced configuration options for biobb_gromacs MakeNdx
    doc: |-
      Advanced configuration options for biobb_gromacs MakeNdx. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_gromacs MakeNdx documentation: https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.make_ndx
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/make_ndx.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
baseCommand: nma_run

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/flexserv/structure.ca.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_log_path:
    label: Output log file
    doc: |-
      Output log file
      Type: string
      File type: output
      Accepted formats: log, out, txt, o
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/nma_run_out.log
    type: string
    format:
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    - edam:format_2330
    inputBinding:
      position: 2
      prefix: --output_log_path
    default: system.log

  output_crd_path:
    label: Output ensemble
    doc: |-
      Output ensemble
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/flexserv/nma_run_out.crd
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 3
      prefix: --output_crd_path
    default: system.crd

  config:
    label: Advanced configuration options for biobb_flexserv NMARun
    doc: |-
      Advanced configuration options for biobb_flexserv NMARun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv NMARun documentation: https://biobb-flexserv.readthedocs.io/en/latest/flexserv.html#module-flexserv.nma_run
    type: string?
    inputBinding:
      prefix: --config
CWL NMA From line 11 of biobb_adapters/nma_run.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
baseCommand: nolb_nma

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output multi-model PDB file with the generated ensemble
    doc: |-
      Output multi-model PDB file with the generated ensemble
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/nolb_output.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_flexdyn Nolb_nma
    doc: |-
      Advanced configuration options for biobb_flexdyn Nolb_nma. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn Nolb_nma documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.nolb
    type: string?
    inputBinding:
      prefix: --config
CWL nolb From line 11 of biobb_adapters/nolb_nma.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
baseCommand: pcz_animate

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_crd_path:
    label: Output PCA animated trajectory file
    doc: |-
      Output PCA animated trajectory file
      Type: string
      File type: output
      Accepted formats: crd, mdcrd, inpcrd, pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcazip_anim1.pdb
    type: string
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_crd_path
    default: system.crd

  config:
    label: Advanced configuration options for biobb_flexserv PCZanimate
    doc: |-
      Advanced configuration options for biobb_flexserv PCZanimate. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZanimate documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_animate
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/pcz_animate.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
baseCommand: pcz_bfactor

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_dat_path:
    label: Output Bfactor x residue x PCA mode file
    doc: |-
      Output Bfactor x residue x PCA mode file
      Type: string
      File type: output
      Accepted formats: dat, txt, csv
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/bfactors.dat
    type: string
    format:
    - edam:format_1637
    - edam:format_2330
    - edam:format_3752
    inputBinding:
      position: 2
      prefix: --output_dat_path
    default: system.dat

  output_pdb_path:
    label: Output PDB with Bfactor x residue x PCA mode file
    doc: |-
      Output PDB with Bfactor x residue x PCA mode file
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/bfactors.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_flexserv PCZbfactor
    doc: |-
      Advanced configuration options for biobb_flexserv PCZbfactor. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZbfactor documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_bfactor
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/pcz_bfactor.cwl 
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
baseCommand: pcz_collectivity

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_json_path:
    label: Output json file with PCA Collectivity indexes per mode
    doc: |-
      Output json file with PCA Collectivity indexes per mode
      Type: string
      File type: output
      Accepted formats: json
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_collectivity.json
    type: string
    format:
    - edam:format_3464
    inputBinding:
      position: 2
      prefix: --output_json_path
    default: system.json

  config:
    label: Advanced configuration options for biobb_flexserv PCZcollectivity
    doc: |-
      Advanced configuration options for biobb_flexserv PCZcollectivity. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZcollectivity documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcc_collectivity
    type: string?
    inputBinding:
      prefix: --config
CWL JSON From line 12 of biobb_adapters/pcz_collectivity.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
baseCommand: pcz_evecs

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_json_path:
    label: Output json file with PCA Eigen Vectors
    doc: |-
      Output json file with PCA Eigen Vectors
      Type: string
      File type: output
      Accepted formats: json
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_evecs.json
    type: string
    format:
    - edam:format_3464
    inputBinding:
      position: 2
      prefix: --output_json_path
    default: system.json

  config:
    label: Advanced configuration options for biobb_flexserv PCZevecs
    doc: |-
      Advanced configuration options for biobb_flexserv PCZevecs. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZevecs documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_evecs
    type: string?
    inputBinding:
      prefix: --config
CWL JSON From line 11 of biobb_adapters/pcz_evecs.cwl 
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
baseCommand: pcz_hinges

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_json_path:
    label: Output hinge regions x PCA mode file
    doc: |-
      Output hinge regions x PCA mode file
      Type: string
      File type: output
      Accepted formats: json
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/hinges.json
    type: string
    format:
    - edam:format_3464
    inputBinding:
      position: 2
      prefix: --output_json_path
    default: system.json

  config:
    label: Advanced configuration options for biobb_flexserv PCZhinges
    doc: |-
      Advanced configuration options for biobb_flexserv PCZhinges. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZhinges documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_hinges
    type: string?
    inputBinding:
      prefix: --config
CWL JSON From line 12 of biobb_adapters/pcz_hinges.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
baseCommand: pcz_info

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_json_path:
    label: Output json file with PCA info such as number of components, variance and
      dimensionality
    doc: |-
      Output json file with PCA info such as number of components, variance and dimensionality
      Type: string
      File type: output
      Accepted formats: json
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_info.json
    type: string
    format:
    - edam:format_3464
    inputBinding:
      position: 2
      prefix: --output_json_path
    default: system.json

  config:
    label: Advanced configuration options for biobb_flexserv PCZinfo
    doc: |-
      Advanced configuration options for biobb_flexserv PCZinfo. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZinfo documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_info
    type: string?
    inputBinding:
      prefix: --config
CWL JSON From line 11 of biobb_adapters/pcz_info.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
baseCommand: pcz_stiffness

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pcz_path:
    label: Input compressed trajectory file
    doc: |-
      Input compressed trajectory file
      Type: string
      File type: input
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz
    type: File
    format:
    - edam:format_3874
    inputBinding:
      position: 1
      prefix: --input_pcz_path

  output_json_path:
    label: Output json file with PCA Stiffness
    doc: |-
      Output json file with PCA Stiffness
      Type: string
      File type: output
      Accepted formats: json
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_stiffness.json
    type: string
    format:
    - edam:format_3464
    inputBinding:
      position: 2
      prefix: --output_json_path
    default: system.json

  config:
    label: Advanced configuration options for biobb_flexserv PCZstiffness
    doc: |-
      Advanced configuration options for biobb_flexserv PCZstiffness. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZstiffness documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_stiffness
    type: string?
    inputBinding:
      prefix: --config
CWL JSON From line 11 of biobb_adapters/pcz_stiffness.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
baseCommand: pcz_zip

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexserv:4.0.2--pypl5321hdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/structure.ca.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  input_crd_path:
    label: Input Trajectory file
    doc: |-
      Input Trajectory file
      Type: string
      File type: input
      Accepted formats: crd, mdcrd, inpcrd
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/traj.crd
    type: File
    format:
    - edam:format_3878
    - edam:format_3878
    - edam:format_3878
    inputBinding:
      position: 2
      prefix: --input_crd_path

  output_pcz_path:
    label: Output compressed trajectory
    doc: |-
      Output compressed trajectory
      Type: string
      File type: output
      Accepted formats: pcz
      Example file: https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcazip.pcz
    type: string
    format:
    - edam:format_3874
    inputBinding:
      position: 3
      prefix: --output_pcz_path
    default: system.pcz

  config:
    label: Advanced configuration options for biobb_flexserv PCZzip
    doc: |-
      Advanced configuration options for biobb_flexserv PCZzip. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexserv PCZzip documentation: https://biobb-flexserv.readthedocs.io/en/latest/pcasuite.html#module-pcasuite.pcz_zip
    type: string?
    inputBinding:
      prefix: --config
CWL From line 11 of biobb_adapters/pcz_zip.cwl 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
baseCommand: prody_anm

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/biobb_flexdyn:4.0.3--pyhdfd78af_0

inputs:
  input_pdb_path:
    label: Input PDB file
    doc: |-
      Input PDB file
      Type: string
      File type: input
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure.pdb
    type: File
    format:
    - edam:format_1476
    inputBinding:
      position: 1
      prefix: --input_pdb_path

  output_pdb_path:
    label: Output multi-model PDB file with the generated ensemble
    doc: |-
      Output multi-model PDB file with the generated ensemble
      Type: string
      File type: output
      Accepted formats: pdb
      Example file: https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/prody/prody_output.pdb
    type: string
    format:
    - edam:format_1476
    inputBinding:
      position: 2
      prefix: --output_pdb_path
    default: system.pdb

  config:
    label: Advanced configuration options for biobb_flexdyn ProdyANM
    doc: |-
      Advanced configuration options for biobb_flexdyn ProdyANM. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_flexdyn ProdyANM documentation: https://biobb-flexdyn.readthedocs.io/en/latest/flexdyn.html#module-flexdyn.prody_anm
    type: string?
    inputBinding:
      prefix: --config
CWL ProDy From line 11 of biobb_adapters/prody_anm.cwl
ShowHide 15 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/bioexcel/biobb_workflows/tree/master/biobb_wf_flexdyn/cwl
Name: cwl-protein-conformational-ensembles-generation
Version: Version 2
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: None
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57