diff COBRAxy/custom_data_generator.py @ 363:941ff9b896e4 draft

Uploaded

--- a/COBRAxy/custom_data_generator.py	Thu Sep 04 23:34:37 2025 +0000
+++ b/COBRAxy/custom_data_generator.py	Thu Sep 04 23:39:51 2025 +0000
@@ -38,13 +38,13 @@
     parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True,
                         help="Output format: CSV (tabular) or Excel (xlsx)")
     
-    parser.add_argument('-idop', '--output_path', type = str, default='result', 
-                        help = 'output path for the result files (default: result)')
+    parser.add_argument("--out_data", type=str, required=True,
+                        help="Output file for the merged dataset (CSV or XLSX)")
+
     
     parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
-                    help="Tool directory (passed from Galaxy as $__tool_directory__)")
+                        help="Tool directory (passed from Galaxy as $__tool_directory__)")
 
-    
 
     return parser.parse_args(args)
 
@@ -255,14 +255,13 @@
 
 
     ####
-    out_data_path = ARGS.output_path  # Galaxy provides a filepath
+    out_data_path = ARGS.out_data  # Galaxy provides a filepath
 
     if ARGS.output_format == "xlsx":
         merged.to_excel(out_data_path, index=False)
     else:
         merged.to_csv(out_data_path, sep="\t", index=False)
 
-    print(f"Custom data generated for model '{model_name}' and saved to '{out_data_path}'")
 
 
 if __name__ == '__main__':