Mercurial > repos > bimib > cobraxy

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

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Uploaded
author francesco_lapi
date Fri, 05 Sep 2025 06:06:08 +0000
parents 72f592fe1f7d
children f4b83b3a3486
comparison
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374:5c98a5cd8bd8 375:130043620f8d
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_data", type=str, 42 parser.add_argument("--out_tabular", type=str,
43 help="Output file for the merged dataset (CSV or XLSX)")
44
45 parser.add_argument("--out_xlsx", type=str,
43 help="Output file for the merged dataset (CSV or XLSX)") 46 help="Output file for the merged dataset (CSV or XLSX)")
44 47
45 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__), 48 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
46 help="Tool directory (passed from Galaxy as $__tool_directory__)") 49 help="Tool directory (passed from Galaxy as $__tool_directory__)")
47 50
255 258
256 259
257 #### 260 ####
258 261
259 if ARGS.output_format == "xlsx": 262 if ARGS.output_format == "xlsx":
260 #if not ARGS.out_xlsx.lower().endswith(".xlsx"): 263 if not ARGS.out_xlsx:
261 # ARGS.out_xlsx += ".xlsx" 264 raise utils.ArgsErr("out_xlsx", "output path (--out_xlsx) is required when output_format == xlsx", ARGS.out_xlsx)
262 265 if not ARGS.out_xlsx.lower().endswith(".xlsx"):
263 merged.to_excel(ARGS.out_data, index=False) 266 ARGS.out_xlsx += ".xlsx"
267 merged.to_excel(ARGS.out_xlsx, index=False, sheet_name='Sheet_name_1')
264 else: 268 else:
265 merged.to_csv(ARGS.out_data, sep="\t", index=False) 269 if not ARGS.out_tabular:
270 raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
271 merged.to_csv(ARGS.out_tabular, sep="\t", index=False)
266 272
267 print("CustomDataGenerator: completed successfully") 273 print("CustomDataGenerator: completed successfully")
268 274
269 if __name__ == '__main__': 275 if __name__ == '__main__':
270 main() 276 main()