remove unused fake news inputs

jfennick · jfennick · commit e39cdbf5b067 · 2024-04-04T07:26:36.000-10:00
diff --git a/cwl_adapters/autodock_vina_filter.cwl b/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:
diff --git a/cwl_adapters/autodock_vina_rescore.cwl b/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
diff --git a/cwl_adapters/config_tag/config_tag_box.cwl b/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.
diff --git a/cwl_adapters/config_tag/config_tag_mdp.cwl b/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.
diff --git a/cwl_adapters/config_tag/config_tag_pdb.cwl b/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.
diff --git a/cwl_adapters/config_tag/config_tag_pdb2gmx.cwl b/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.
diff --git a/cwl_adapters/diffdock.cwl b/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:
diff --git a/cwl_adapters/duplicate.cwl b/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
diff --git a/cwl_adapters/duplicate2D.cwl b/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
diff --git a/cwl_adapters/extract_pdbbind_refined.cwl b/cwl_adapters/extract_pdbbind_refined.cwl
@@ -75,28 +75,6 @@ inputs:
       position: 5
     default: system.log
 
-  output_pdb_paths:
-    label: Path to the input file
-    doc: |-
-      Path to the input file
-      Type: string
-      File type: input
-      Accepted formats: pdb
-    type: string?
-    format:
-    - edam:format_1476 # pdb
-
-  output_sdf_paths:
-    label: Path to the input file
-    doc: |-
-      Path to the input file
-      Type: string
-      File type: input
-      Accepted formats: sdf
-    type: string?
-    format:
-    - edam:format_3814 # sdf
-
   min_row:
     label: The row min index
     doc: |-
@@ -132,21 +110,6 @@ inputs:
       position: 8
     default: False
 
-  experimental_dGs:
-    label: Experimental Free Energies of Binding
-    doc: |-
-      Experimental Free Energies of Binding
-    type: string?
-    format:
-    - edam:format_2330
-    
-  pdb_ids:
-    label: The PDBID of proteins
-    doc: |-
-      The PDBID of proteins
-    type: string?
-    format:
-    - edam:format_2330
 outputs:
 
   output_txt_path:
diff --git a/cwl_adapters/generate_conformers.cwl b/cwl_adapters/generate_conformers.cwl
@@ -122,14 +122,6 @@ inputs:
       prefix: --convert_Kd_dG
     default: False
 
-  experimental_dGs:
-    label: Experimental Free Energies of Binding
-    doc: |-
-      Experimental Free Energies of Binding
-    type: string?
-    format:
-    - edam:format_2330
-
 outputs:
   output_txt_path:
     label: Path to the txt file
diff --git a/cwl_adapters/onionnet-sfct.cwl b/cwl_adapters/onionnet-sfct.cwl
@@ -55,14 +55,9 @@ inputs:
       prefix: -o
     default: "sfct.txt"
 
+# Is this still necessary?
   output_path:
-    type: string?
-
-  output_docking_score:
-    type: string?
-
-  output_poses_rescore:
-    type: string?
+    type: string
 
 outputs:
 
diff --git a/cwl_adapters/python3_calculate_net_charge.cwl b/cwl_adapters/python3_calculate_net_charge.cwl
@@ -65,14 +65,6 @@ inputs:
       position: 4
     default: system.log
 
-  net_charge:
-    label: Calculated total charge
-    doc: |-
-      Calculated total charge
-    type: string
-    format:
-    - edam:format_2330
-
 outputs:
   output_log_path:
     label: Path to the log file
diff --git a/cwl_adapters/rank_diffdock_poses.cwl b/cwl_adapters/rank_diffdock_poses.cwl
@@ -43,9 +43,6 @@ inputs:
     # set default to keep all poses
     default: 100
 
-  output_poses:
-    type: string?
-
 outputs:
 
   output_poses:
diff --git a/cwl_adapters/sanitize_ligand.cwl b/cwl_adapters/sanitize_ligand.cwl
@@ -29,12 +29,6 @@ inputs:
     inputBinding:
       prefix: --input_small_mol_ligand
 
-  output_ligand:
-    type: string?
-
-  valid_ligand:
-    type: string?
-
 outputs:
 
   output_ligand:
diff --git a/cwl_adapters/smina_docking.cwl b/cwl_adapters/smina_docking.cwl
@@ -87,8 +87,9 @@ inputs:
       prefix: -o
     default: "docked.pdb"
 
+# Is this still necessary?
   output_path:
-    type: string?
+    type: string
     
 outputs:
   
