refactor duplicate

utils/duplicate-plugin/ict.yml → utils/pre-process/structure-change/duplicate-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: duplicate
 version: 0.1.0
-container: duplicate-plugin
+container: duplicate-tool
 entrypoint:
 title: duplicate
 description: Duplicates a pdbqt file n times, where n is the length of another array.
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/pre-process/structure-change/duplicate-tool/tests/test_duplicate.py

@@ -0,0 +1,32 @@
+"""Tests for duplicate."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_duplicate() -> None:
+    """Test pdb."""
+    # Define paths and input properties
+    cwl_file_str = "duplicate_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_pdbqt_singleton_path = Path(__file__).resolve().parent / Path(
+        "1msn_protein.pdb",
+    )
+    repeats = 2
+
+    # Create the CWL step
+    duplicate_step = Step(clt_path=cwl_file)
+    duplicate_step.input_pdbqt_singleton_path = input_pdbqt_singleton_path
+
+    # Prepare the input_pdbqt_array_path with duplicates
+    file_dict = {"path": str(input_pdbqt_singleton_path)}
+    duplicate_step.input_pdbqt_array_path = [file_dict.copy() for _ in range(repeats)]
+
+    # Create the workflow and run it
+    steps = [duplicate_step]
+    filename = "duplicate_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # cant capture stdout to check status