Merge pull request PolusAI#22 from jfennick/custom_tag_explicit_edge_syntax

use custom yaml tags !& !*

Author: sameeul

.vscode/settings.json

@@ -1,16 +1,24 @@
 {
     "mypy.runUsingActiveInterpreter": true,
-    "python.linting.mypyEnabled": true,
-    "python.linting.pylintEnabled": true,
-    "python.formatting.provider": "autopep8",
-    "python.formatting.autopep8Args": [
+    "mypy.enabled": true,
+    "pylint.args": ["--max-line-length=120"],
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.autopep8",
+        "editor.formatOnSave": false
+    },
+    "autopep8.args": [
         "--max-line-length",
         "120"
     ],
     "gitlens.hovers.enabled": false,
     "yaml.schemas": {
         "../workflow-inference-compiler/autogenerated/schemas/wic.json": "*.yml"
     },
+    "yaml.customTags": [
+        "!&",
+        "!*",
+        "!ii"
+    ],
     "[yaml]": {
         "editor.suggest.showWords": false
     },

cwl_adapters/autodock_vina_filter.cwl

@@ -182,30 +182,6 @@ inputs:
     - edam:format_1476
     default: .
 
-  docking_scores:
-    label: Estimated Free Energies of Binding
-    doc: |-
-      Estimated Free Energies of Binding
-    type: string?
-    format:
-    - edam:format_2330
-
-  experimental_binding_data:
-    label: Experimental binding data (if any)
-    doc: |-
-      Experimental binding data (if any)
-    type: string?
-    format:
-    - edam:format_2330
-
-  experimental_dGs:
-    label: Experimental binding free energy dG values (if any)
-    doc: |-
-      Experimental binding free energy dG values (if any)
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
 # NOTE: If docking_score_cutoff is too negative and filters out all of the files,
 # you will get the following runtime error message:

cwl_adapters/autodock_vina_rescore.cwl

@@ -107,14 +107,6 @@ inputs:
     - edam:format_2330
     default: system.log
 
-  docking_score:
-    label: Estimated Free Energy of Binding
-    doc: |-
-      Estimated Free Energy of Binding
-    type: string
-    format:
-    - edam:format_2330
-
 outputs:
   output_ligand_pdbqt_path:
     label: Path to the output PDBQT files

cwl_adapters/config_tag/config_tag_box.cwl

@@ -22,14 +22,6 @@ inputs:
 
 # TODO: box_coordinates
 
-  output_config_string:
-    label: A dictionary of the given arguments as a JSON-encoded string.
-    doc: |-
-      A dictionary of the given arguments as a JSON-encoded string.
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
   output_config_string:
     label: A dictionary of the given arguments as a JSON-encoded string.

cwl_adapters/config_tag/config_tag_mdp.cwl

@@ -46,14 +46,6 @@ inputs:
       The nominal pressure
     type: float
 
-  output_config_string:
-    label: A dictionary of the given arguments as a JSON-encoded string.
-    doc: |-
-      A dictionary of the given arguments as a JSON-encoded string.
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
   output_config_string:
     label: A dictionary of the given arguments as a JSON-encoded string.

cwl_adapters/config_tag/config_tag_pdb.cwl

@@ -20,14 +20,6 @@ inputs:
   filter:
     type: string?
 
-  output_config_string:
-    label: A dictionary of the given arguments as a JSON-encoded string.
-    doc: |-
-      A dictionary of the given arguments as a JSON-encoded string.
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
   output_config_string:
     label: A dictionary of the given arguments as a JSON-encoded string.

cwl_adapters/config_tag/config_tag_pdb2gmx.cwl

@@ -34,14 +34,6 @@ inputs:
 
 # TODO: his
 
-  output_config_string:
-    label: A dictionary of the given arguments as a JSON-encoded string.
-    doc: |-
-      A dictionary of the given arguments as a JSON-encoded string.
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
   output_config_string:
     label: A dictionary of the given arguments as a JSON-encoded string.

cwl_adapters/diffdock.cwl

@@ -81,12 +81,6 @@ inputs:
       prefix: --complex_name
     default:  outputs
 
-  output_files:
-    type: string?
-
-  max_confident_pose:
-    type: string?
-
 outputs:
 
   max_confident_pose:

cwl_adapters/duplicate.cwl

@@ -39,19 +39,6 @@ inputs:
     format:
     - edam:format_1476
 
-  output_pdbqt_path:
-    label: Path to the output PDBQT files
-    doc: |-
-      Path to the output PDBQT files
-      Type: string
-      File type: output
-      Accepted formats: pdbqt
-      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
-    type: string
-    format:
-    - edam:format_1476
-    default: .
-
 outputs:
   output_pdbqt_path:
     label: Path to the output PDBQT files

cwl_adapters/duplicate2D.cwl

@@ -39,19 +39,6 @@ inputs:
     format:
     - edam:format_1476
 
-  output_pdbqt_path:
-    label: Path to the output PDBQT files
-    doc: |-
-      Path to the output PDBQT files
-      Type: string
-      File type: output
-      Accepted formats: pdbqt
-      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
-    type: string
-    format:
-    - edam:format_1476
-    default: .
-
 outputs:
   output_pdbqt_path:
     label: Path to the output PDBQT files