create pdb dat file on the fly

Author: ndonyapour

Diff for: .github/workflows/docker_build.yml

@@ -26,7 +26,8 @@ jobs:
                      rename_residues_mol, combine_structure,
                      remove_terminal_residue_name_prefixes, molgan,
                      pdbbind_refined, onionnet-sfct, smina, pdbfixer,
-                     fix_pdb_atom_column, extract_protein, generate_conformers]  # No username for pdbind_refined
+                     fix_pdb_atom_column, extract_protein, generate_conformers,
+                     onionnet, combine_pdb, rename_residues_pdb]  # No username for pdbind_refined
         # skip data/ and cwl_adapters/file_format_conversions/biosimspace/
     runs-on: [ubuntu-latest]
 

Diff for: cwl_adapters/combine_pdb.cwl

@@ -0,0 +1,72 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+doc: |-
+  A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+baseCommand: ['python', '/combine_pdb.py']
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/combine_pdb
+
+inputs:
+  input_structure1:
+    label: Input PDB structure 1 file path
+    doc: |-
+      Input PDB structure 1 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure1
+
+  input_structure2:
+    label: Input PDB structure 2 file path
+    doc: |-
+      Input PDB structure 2 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure2
+
+  output_structure_path:
+    label: Output combined PDB file path
+    doc: |-
+      Output combined PDB file path
+      Type: string
+      File type: output
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb
+    type: string
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --output_structure_path
+    default: system.pdb
+outputs:
+  output_structure_path:
+    label: Output protein file path
+    doc: |-
+      Output protein file path
+    type: File
+    outputBinding:
+      glob: $(inputs.output_structure_path)
+    format: edam:format_1476
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

Diff for: cwl_adapters/onionnet-feature.cwl

@@ -0,0 +1,70 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: Generate the features for the protein-ligand complexes using OnionNet V1
+
+baseCommand: ["python", "/onionnet/generate_features.py"]
+arguments: ["-inp", "input.dat"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/onionnet
+
+requirements:
+  - class: InlineJavascriptRequirement
+  # This enables staging input files and dynamically generating a file
+  # containing the file paths on the fly.
+  - class: InitialWorkDirRequirement 
+    listing: |
+      ${
+        var dat_file_contents = "";
+        for (var i = 0; i < inputs.pdb_paths.length; i++) {
+          dat_file_contents += inputs.pdb_paths[i].path + "\n";
+        }
+        // Note: Uses https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
+        // and https://www.commonwl.org/user_guide/topics/creating-files-at-runtime.html
+        // "If the value is a string literal or an expression which evaluates to a string, 
+        // a new file must be created with the string as the file contents."
+        return ([{"entryname": "input.dat", "entry": dat_file_contents}]);
+      }
+
+inputs:
+  pdb_paths:
+    label: The path of input pdb files
+    type: File[]
+    format: 
+    - edam:format_1476 # PDB
+
+  num_of_cpus:
+    label: number of CPUs to use.
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -nt
+    default: 1
+
+  output_feature_file:
+    label: the output file name containing the features.
+    type: string?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -out
+    default: "output.csv"
+
+outputs:
+  output_feature_file:
+    type: File
+    format: edam:format_3752
+    outputBinding:
+      glob: $(inputs.output_feature_file)
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl