diff generate_manifest.py @ 8:012191b79fda draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 6413a461059c4a421a7812a08f244c224cde8ee2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_manifest.py	Fri Oct 17 16:22:03 2025 +0000
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+#
+# Generates a FragPipe Manifest file.
+#
+
+import argparse
+import csv
+
+# The three columns for each scanfile are "Experiment, Bioreplicate, and Data type
+column_types = ('exp', 'bio', 'type')
+output_filename = 'fp.manifest'
+
+
+# Add column values to a list of rows for each scan file.
+def add_column(column_type, args, rows):
+    nfiles = len(args.scanfiles)
+
+    # Each scan file is numbered 1 through n in column
+    if getattr(args, f'{column_type}_consec'):
+        vals = range(1, nfiles + 1)
+
+    # All scan files have same value in column
+    elif getattr(args, f'{column_type}_assign_all'):
+        vals = [getattr(args, f'{column_type}_assign_all')] * nfiles
+
+    # Values are provided for scan files in a comma-delimited list
+    elif getattr(args, f'{column_type}_col'):
+        vals = getattr(args, f'{column_type}_col').split(',')
+        if len(vals) != nfiles:
+            raise ValueError((f'Incorrect number of values entered for column {column_type}. '
+                              'Exactly one value must be entered for each scan file.'))
+
+    # Otherwise, this column remains empty.
+    else:
+        vals = [''] * nfiles
+
+    for i, row in enumerate(rows):
+        row.append(vals[i])
+
+
+def main():
+    parser = argparse.ArgumentParser()
+
+    # Each column has the same methods for populating
+    for column_type in column_types:
+        parser.add_argument(f'--{column_type}-consec', action='store_true')
+        parser.add_argument(f'--{column_type}-assign-all')
+        parser.add_argument(f'--{column_type}-col')
+
+    # Scanfile names, which should be identical to history identifiers
+    parser.add_argument('scanfiles', nargs='+')
+
+    args = parser.parse_args()
+
+    # Create and populate data structure for tabular output
+    rows = [[scanfile] for scanfile in args.scanfiles]
+    for column_type in column_types:
+        add_column(column_type, args, rows)
+
+    # Write out manifest file.
+    # Use mode=a as the script will be called once for each scan group.
+    with open(output_filename, mode='a') as outf:
+        manifest_writer = csv.writer(outf, delimiter='\t')
+        for row in rows:
+            manifest_writer.writerow(row)
+
+
+if __name__ == "__main__":
+    main()