diff COBRAxy/custom_data_generator.py @ 375:130043620f8d draft

Uploaded

--- a/COBRAxy/custom_data_generator.py	Fri Sep 05 05:54:54 2025 +0000
+++ b/COBRAxy/custom_data_generator.py	Fri Sep 05 06:06:08 2025 +0000
@@ -39,7 +39,10 @@
     parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True,
                         help="Output format: CSV (tabular) or Excel (xlsx)")
     
-    parser.add_argument("--out_data", type=str,
+    parser.add_argument("--out_tabular", type=str,
+                        help="Output file for the merged dataset (CSV or XLSX)")
+    
+    parser.add_argument("--out_xlsx", type=str,
                         help="Output file for the merged dataset (CSV or XLSX)")
     
     parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
@@ -257,12 +260,15 @@
     ####
 
     if ARGS.output_format == "xlsx":
-        #if not ARGS.out_xlsx.lower().endswith(".xlsx"):
-        #    ARGS.out_xlsx += ".xlsx"
-
-        merged.to_excel(ARGS.out_data, index=False)
+        if not ARGS.out_xlsx:
+            raise utils.ArgsErr("out_xlsx", "output path (--out_xlsx) is required when output_format == xlsx", ARGS.out_xlsx)
+        if not ARGS.out_xlsx.lower().endswith(".xlsx"):
+            ARGS.out_xlsx += ".xlsx"
+        merged.to_excel(ARGS.out_xlsx, index=False, sheet_name='Sheet_name_1')
     else:
-        merged.to_csv(ARGS.out_data, sep="\t", index=False)
+        if not ARGS.out_tabular:
+            raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
+        merged.to_csv(ARGS.out_tabular, sep="\t", index=False)
 
 print("CustomDataGenerator: completed successfully")