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ndonyapourndonyapour
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add scoring_onionnet workflow
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Diff for: ‎cwl_adapters/autodock_vina.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.1 # See `loadContents: true` below!
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class: CommandLineTool
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label: Wrapper of the AutoDock Vina software.
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doc: |-
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This class performs docking of the ligand to a set of grids describing the target protein via the AutoDock Vina software.
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baseCommand: vina # NOTE: Only version >=1.2 supports --batch!
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arguments:
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# Need to parse box.pdb and pass in each number separately.
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# REMARK BOX CENTER: 0.102 0.019 -0.004 SIZE: 30.195 31.940 27.005
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# - "--dir" # Need to explicitly pass --dir . in --batch mode
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# - "."
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- "--center_x"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[0])
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- "--center_y"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[1])
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- "--center_z"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[2])
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- "--size_x"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[3])
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- "--size_y"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[4])
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- "--size_z"
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- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[5])
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# NOTE: Cannot use a single javascript expression to create the entire arguments list because CWL treats it as a string:
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# "the `arguments` field is not valid because value is a str"
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# ${
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# var words = inputs.input_box_path.contents.split("\n")[0].split(" ");
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# var nums = words.filter(function(s) {return !isNaN(parseFloat(s))});
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# var args = {};
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# args.push("--dir"); // Need to explicitly pass --dir . in --batch mode
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# args.push(".");
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# args.push("--center_x");
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# args.push(nums[0]);
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# args.push("--center_y");
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# args.push(nums[1]);
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# args.push("--center_z");
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# args.push(nums[2]);
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# args.push("--size_x");
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# args.push(nums[3]);
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# args.push("--size_y");
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# args.push(nums[4]);
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# args.push("--size_z");
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# args.push(nums[5]);
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# return args;
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# }
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hints:
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DockerRequirement:
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dockerPull: jakefennick/autodock_vina
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requirements:
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InlineJavascriptRequirement: {}
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inputs:
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input_ligand_pdbqt_path:
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label: Path to the input PDBQT ligand
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doc: |-
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Path to the input PDBQT ligand
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Type: string
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File type: input
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Accepted formats: pdbqt
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Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
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type: File
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format:
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- edam:format_1476
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inputBinding:
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prefix: --ligand
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input_receptor_pdbqt_path:
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label: Path to the input PDBQT receptor
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doc: |-
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Path to the input PDBQT receptor
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Type: string
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File type: input
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Accepted formats: pdbqt
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Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
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type: File
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format:
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- edam:format_1476
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inputBinding:
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#position: 2
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prefix: --receptor
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input_box_path:
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label: Path to the PDB containing the residues belonging to the binding site
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doc: |-
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Path to the PDB containing the residues belonging to the binding site
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Type: string
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File type: input
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Accepted formats: pdb
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Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
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type: File
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format:
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- edam:format_1476
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# inputBinding:
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# position: 3
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# prefix: --input_box_path
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loadContents: true # requires cwlVersion: v1.1
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# See https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog
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# Curiously, cwlVersion: v1.0 allows loadContents for outputs, but not inputs.
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output_pdbqt_path:
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label: Path to the output PDBQT file
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doc: |-
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Path to the output PDBQT file
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Type: string
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File type: output
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Accepted formats: pdbqt
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Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
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type: string
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format:
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- edam:format_1476
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inputBinding:
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prefix: --out
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default: system.pdbqt
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output_log_path:
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label: Path to the log file
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doc: |-
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Path to the log file
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Type: string
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File type: output
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Accepted formats: log
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Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
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type: string
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format:
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- edam:format_2330
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default: system.log
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cpu:
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label: The number of CPUs to use
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doc: |-
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The number of CPUs to use
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Type: int
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type: int?
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format:
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- edam:format_2330
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inputBinding:
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prefix: --cpu
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default: 1
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exhaustiveness:
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label: exhaustiveness of the global search (roughly proportional to time).
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doc: |-
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exhaustiveness of the global search (roughly proportional to time).
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Type: int
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type: int?
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format:
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- edam:format_2330
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inputBinding:
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prefix: --exhaustiveness
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default: 8
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num_modes:
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label: maximum number of binding modes to generate
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doc: |-
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Tmaximum number of binding modes to generate
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Type: int
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type: int?
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format:
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- edam:format_2330
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inputBinding:
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prefix: --num_modes
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default: 9
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min_rmsd:
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label: The minimum RMSD between output poses
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doc: |-
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The minimum RMSD between output poses
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Type: int
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type: int?
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format:
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- edam:format_2330
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inputBinding:
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prefix: --min_rmsd
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default: 1
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energy_range:
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label: maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
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doc: |-
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maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
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Type: int
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type: int?
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format:
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- edam:format_2330
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inputBinding:
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prefix: --energy_range
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default: 3
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outputs:
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output_pdbqt_path:
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label: Path to the output PDBQT file
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doc: |-
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Path to the output PDBQT file
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type: File
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outputBinding:
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glob: $(inputs.output_pdbqt_path)
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format: edam:format_1476
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output_log_path:
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label: Path to the log file
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doc: |-
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Path to the log file
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type: File
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outputBinding:
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glob: $(inputs.output_log_path)
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format: edam:format_2330
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stdout: $(inputs.output_log_path)
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$namespaces:
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edam: https://edamontology.org/
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$schemas:
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- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

Diff for: ‎cwl_adapters/convert_pdb.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: CommandLineTool
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label: This class is a wrapper of the Open Babel tool.
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doc: |-
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Small molecule format conversion for structures or trajectories. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Visit the official page.
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baseCommand: obabel
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#Usage:
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#obabel[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
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#...
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#Options, other than -i -o -O -m, must come after the input files.
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arguments: [$(inputs.input_path), "-h", "-o", "pdb", "-O", $(inputs.output_pdb_path)]
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# NOTE: These arguments must be given individually; they cannot be concatenated together.
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# (e.g. -xrhn) Otherwise, all but the first argument will be silently ignored!
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# pdb format options
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# Read Options e.g. -as
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# s Output single bonds only
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# b Disable bonding entirely
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# c Ignore CONECT records
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# Write Options, e.g. -xo
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# n Do not write duplicate CONECT records to indicate bond order
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# o Write origin in space group label (CRYST1 section)
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hints:
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DockerRequirement:
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dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1
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requirements:
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InlineJavascriptRequirement: {}
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inputs:
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first_molecule:
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label: Index of the first molecule (1-based)
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doc: |-
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Input Index of the first molecule (1-based)
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Type: string?
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type: string?
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format:
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- edam:format_2330 # 'Textual format'
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inputBinding:
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prefix: -f
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last_molecule:
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label: Index of the last molecule (1-based)
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doc: |-
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Input Index of the last molecule (1-based)
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Type: string?
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type: string?
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format:
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- edam:format_2330 # 'Textual format'
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inputBinding:
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prefix: -l
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input_path:
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label: Path to the input file
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doc: |-
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Path to the input file
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Type: string
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File type: input
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Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc
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Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi
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type: File
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format:
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- edam:format_1637
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- edam:format_1476
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- edam:format_1929
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- edam:format_1929
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- edam:format_2033
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- edam:format_3878
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- edam:format_2030
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- edam:format_1477
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- edam:format_3815
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- edam:format_1477
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- edam:format_3815
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- edam:format_3816
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- edam:format_1476
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- edam:format_1476
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- edam:format_3603
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- edam:format_3814
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- edam:format_1196
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- edam:format_1196
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- edam:format_2033
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- edam:format_2332
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- edam:format_3875
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output_pdb_path:
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label: Path to the output file
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doc: |-
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Path to the output file
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Type: string
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File type: output
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Accepted formats: pdb
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type: string
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format:
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- edam:format_1476 # pdb
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default: system.pdb
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arg1:
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label: Additional arguments
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doc: |-
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Additional arguments
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Type: string?
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type: string?
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format:
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- edam:format_2330 # 'Textual format'
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inputBinding:
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position: 1
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outputs:
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output_pdb_path:
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label: Path to the output file
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doc: |-
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Path to the output file
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type: File
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outputBinding:
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glob: $(inputs.output_pdb_path)
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format: edam:format_1476 # pdb
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$namespaces:
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edam: https://edamontology.org/
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$schemas:
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- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

Diff for: ‎cwl_adapters/onionnet_featurize.cwl

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label: Generate the features for the protein-ligand complexes using OnionNet V1
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baseCommand: ["python", "/onionnet/generate_features.py"]
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baseCommand: ["conda", "run", "-n", "py37", "python", "/onionnet/generate_features.py"]
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arguments: ["-inp", "input.dat"]
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hints:

Diff for: ‎cwl_adapters/onionnet_score.cwl

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label: OnionNet (version1) for rescoring of docking poses
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baseCommand: ["python", "/onionnet/predict.py"]
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baseCommand: ["conda", "run", "-n", "py37", "python", "/onionnet/predict.py"]
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hints:
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DockerRequirement:

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