Merge pull request PolusAI#250 from ndonyapour/boolstr_to_bool

replace boolean string with boolean

Author: sameeul

cwl_adapters/autodock_vina_filter.cwl

@@ -13,7 +13,7 @@ baseCommand: python3
 
 hints:
   DockerRequirement:
-    dockerPull: jakefennick/autodock_vina_filter
+    dockerPull: ndonyapour/autodock_vina_filter
 
 requirements:
   InlineJavascriptRequirement: {}
@@ -115,7 +115,7 @@ inputs:
     label: Use True if autodock vina was run with --rescore
     doc: |-
       Use True if autodock vina was run with --rescore
-    type: string?
+    type: boolean?
     format:
     - edam:format_2330
     inputBinding:

cwl_adapters/config_tag/config_tag_pdb.cwl

@@ -16,9 +16,10 @@ inputs:
     type: string
     format:
     - edam:format_2330
-
+  # Note: Even though the "filter" argument has a boolean type, it cannot accept the value True.
+  # https://biobb-io.readthedocs.io/en/latest/api.html#module-api.pdb
   filter:
-    type: string?
+    type: ["null", boolean, {"type": "array", "items": "string"}]
 
 outputs:
   output_config_string:
@@ -32,12 +33,11 @@ outputs:
         ${
           var config = {};
           config["pdb_code"] = inputs.pdb_id;
-          if (inputs.filter == "False") {
-            config["filter"] = false;
-          } else if (inputs.filter == "None") {
-            config["filter"] = null;
-          } else if (inputs.filter) {
-            config["filter"] = inputs.filter;
+          if (inputs.filter == true) {
+            throw new Error("Error! filter doesn't accept True value");
+          }
+          else {
+          config["filter"] = inputs.filter;
           }
           return JSON.stringify(config);
         }

docker/dockerBuild.sh

@@ -20,7 +20,7 @@ sudo docker build --no-cache --pull -f Dockerfile_align_protein_ca_mda -t jakefe
 sudo docker build --no-cache --pull -f Dockerfile_align_protein_ca_pymol -t jakefennick/align_protein_ca_pymol .
 sudo docker build --no-cache --pull -f Dockerfile_atomselect -t jakefennick/atomselect .
 sudo docker build --no-cache --pull -f Dockerfile_autodock_vina -t jakefennick/autodock_vina .
-sudo docker build --no-cache --pull -f Dockerfile_autodock_vina_filter -t jakefennick/autodock_vina_filter .
+sudo docker build --no-cache --pull -f Dockerfile_autodock_vina_filter -t ndonyapour/autodock_vina_filter .
 sudo docker build --no-cache --pull -f Dockerfile_bash_scripts -t jakefennick/bash_scripts .
 sudo docker build --no-cache --pull -f Dockerfile_calculate_net_charge -t jakefennick/calculate_net_charge .
 sudo docker build --no-cache --pull -f Dockerfile_mol2_to_pdbqt -t jakefennick/mol2_to_pdbqt .

dockerPull.sh

@@ -11,7 +11,7 @@ docker pull jakefennick/align_protein_ca_mda
 docker pull jakefennick/align_protein_ca_pymol
 docker pull jakefennick/atomselect
 docker pull jakefennick/autodock_vina
-docker pull jakefennick/autodock_vina_filter
+docker pull ndonyapour/autodock_vina_filter
 docker pull jakefennick/bash_scripts
 docker pull jakefennick/calculate_net_charge
 docker pull jakefennick/generate_conformers

examples/docking/vs_demo_4.wic

@@ -21,7 +21,7 @@ steps:
     scatter: [pdb_id]
     in:
       pdb_id: !* pdbids
-      filter: !ii "False"
+      filter: !ii False
     out:
     - output_config_string: !& pdb_id_str
   pdb:
@@ -94,7 +94,7 @@ steps:
       docking_score_cutoff: !ii -1.0
       max_num_poses_per_ligand: !ii 1
       max_num_poses_total: !ii 1 #25 # Use 1 for CI same as max_row
-      rescore: !ii 'True'
+      rescore: !ii True
       input_ligand_pdbqt_path: !* ligand_rescore.pdbqt
       input_receptor_pdbqt_path: !* receptor_dup_2D.pdb
     out:

examples/scripts/autodock_vina_filter.py

@@ -10,7 +10,7 @@
 parser.add_argument('--docking_score_cutoff', type=float)
 parser.add_argument('--max_num_poses_per_ligand', type=int)
 parser.add_argument('--max_num_poses_total', type=int)
-parser.add_argument('--rescore', type=bool)
+parser.add_argument('--rescore', required=False, action='store_true')
 args = parser.parse_args()
 
 input_log_path = args.input_log_path