Mercurial > repos > bimib > cobraxy

comparison COBRAxy/custom_data_generator.py @ 373:72f592fe1f7d draft

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author francesco_lapi
date Fri, 05 Sep 2025 05:54:35 +0000
parents d0a307c3ae36
children 130043620f8d
comparison
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372:d0a307c3ae36 373:72f592fe1f7d
37 help="Custom medium file if medium_selector=Custom") 37 help="Custom medium file if medium_selector=Custom")
38 38
39 parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True, 39 parser.add_argument("--output_format", type=str, choices=["tabular", "xlsx"], required=True,
40 help="Output format: CSV (tabular) or Excel (xlsx)") 40 help="Output format: CSV (tabular) or Excel (xlsx)")
41 41
42 parser.add_argument("--out_tabular", type=str, 42 parser.add_argument("--out_data", type=str,
43 help="Output file for the merged dataset (CSV or XLSX)")
44
45 parser.add_argument("--out_xlsx", type=str,
46 help="Output file for the merged dataset (CSV or XLSX)") 43 help="Output file for the merged dataset (CSV or XLSX)")
47 44
48 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), 45 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
49 help="Tool directory (passed from Galaxy as $__tool_directory__)") 46 help="Tool directory (passed from Galaxy as $__tool_directory__)")
50 47
261 258
262 if ARGS.output_format == "xlsx": 259 if ARGS.output_format == "xlsx":
263 #if not ARGS.out_xlsx.lower().endswith(".xlsx"): 260 #if not ARGS.out_xlsx.lower().endswith(".xlsx"):
264 # ARGS.out_xlsx += ".xlsx" 261 # ARGS.out_xlsx += ".xlsx"
265 262
266 merged.to_excel(ARGS.out_xlsx, index=False) 263 merged.to_excel(ARGS.out_data, index=False)
267 else: 264 else:
268 merged.to_csv(ARGS.out_tabular, sep="\t", index=False) 265 merged.to_csv(ARGS.out_data, sep="\t", index=False)
269 266
270 print("CustomDataGenerator: completed successfully") 267 print("CustomDataGenerator: completed successfully")
271 268
272 if __name__ == '__main__': 269 if __name__ == '__main__':
273 main() 270 main()