Mercurial > repos > bimib > cobraxy

comparison COBRAxy/metabolicModel2Tabular.py @ 496:6c973150937b draft

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Uploaded
author francesco_lapi
date Tue, 30 Sep 2025 15:26:41 +0000
parents e19083971cc3
children 36838126cc07
comparison
equal deleted inserted replaced
495:e19083971cc3 496:6c973150937b
35 35
36 parser.add_argument("--model", type=str, 36 parser.add_argument("--model", type=str,
37 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)") 37 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)")
38 parser.add_argument("--input", type=str, 38 parser.add_argument("--input", type=str,
39 help="Custom model file (JSON or XML)") 39 help="Custom model file (JSON or XML)")
40 parser.add_argument("--name", type=str, required=True, 40 parser.add_argument("--name", nargs='*', required=True,
41 help="Model name (default or custom)") 41 help="Model name (default or custom)")
42 42
43 parser.add_argument("--medium_selector", type=str, required=True, 43 parser.add_argument("--medium_selector", type=str, required=True,
44 help="Medium selection option") 44 help="Medium selection option")
45 45
179 """ 179 """
180 # Parse args from frontend (Galaxy XML) 180 # Parse args from frontend (Galaxy XML)
181 global ARGS 181 global ARGS
182 ARGS = process_args(args) 182 ARGS = process_args(args)
183 183
184 # Convert name from list to string (handles names with spaces)
185 if isinstance(ARGS.name, list):
186 ARGS.name = ' '.join(ARGS.name)
184 187
185 if ARGS.input: 188 if ARGS.input:
186 # Load a custom model from file 189 # Load a custom model from file
187 model = load_custom_model( 190 model = load_custom_model(
188 utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext) 191 utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)