--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_workflow.py	Fri Jan 16 09:34:00 2026 +0000
@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+
+#
+# Generates a FragPipe Workflow file.
+#
+
+import pathlib
+import sys
+
+default_workflow = sys.argv[1]
+user_params_filename = sys.argv[2]
+output_workflow_filename = sys.argv[3]
+
+# Default workflow as packaged in the Galaxy $__tool_directory__
+default_workflow_path = pathlib.Path(__file__).resolve().parent.joinpath(f'workflows/{default_workflow}.workflow')
+
+# Collect comments separately from parameters
+comments = []
+
+# Dictionary with workflow parameters
+wfdict = {}
+
+# Initialize workflow dictionary with defaults
+with open(default_workflow_path, 'r') as inf:
+    for line in inf:
+        if line.startswith('#'):
+            comments.append(line)
+        elif line.strip() != '':
+            kv = line.strip().split('=')
+            if len(kv) < 2:
+                kv.append('')
+            wfdict[kv[0]] = '='.join(kv[1:])
+
+# Overwrite with user parameters from Galaxy
+with open(user_params_filename, 'r') as inf:
+    for line in inf:
+        if line.strip() != '':
+            kv = line.strip().split('=')
+            if len(kv) < 2:
+                kv.append('')
+            wfdict[kv[0]] = '='.join(kv[1:])
+
+# Output comments and parameter definitions to workflow file
+with open(output_workflow_filename, 'w') as outf:
+    for comment in comments:
+        print(comment, file=outf)
+    for k in sorted(wfdict.keys()):
+        kv = f'{k}={wfdict[k]}'
+        print(kv, file=outf)