Mercurial > repos > tduigou > seq_to_db
comparison save_to_db.py @ 1:3daf04425ea1 draft
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
| author | tduigou |
|---|---|
| date | Thu, 12 Jun 2025 09:04:14 +0000 |
| parents | 9f845ccb1a9f |
| children | dad2c4c3450a |
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| 0:9f845ccb1a9f | 1:3daf04425ea1 |
|---|---|
| 199 parser.add_argument("--table", required=True, help="Table name in the database") | 199 parser.add_argument("--table", required=True, help="Table name in the database") |
| 200 parser.add_argument("--fragment_column", required=True, help="Fragment column name in the database") | 200 parser.add_argument("--fragment_column", required=True, help="Fragment column name in the database") |
| 201 parser.add_argument("--output", required=True, help="Text report") | 201 parser.add_argument("--output", required=True, help="Text report") |
| 202 parser.add_argument("--file_name_mapping", required=True, help="real fragments names") | 202 parser.add_argument("--file_name_mapping", required=True, help="real fragments names") |
| 203 parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters") | 203 parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters") |
| 204 parser.add_argument("--execution_enable", required=True, help="enabbe or desable execution directly from the tool option") | |
| 204 args = parser.parse_args() | 205 args = parser.parse_args() |
| 206 | |
| 207 # enabbe or desable execution based on galaxy param (execution_enable) | |
| 208 | |
| 209 if args.execution_enable == 'false': | |
| 210 print("Execution disabled. 'Send Requenst to DB' is set to 'false'") | |
| 211 return | |
| 205 | 212 |
| 206 # Load JSON config if provided | 213 # Load JSON config if provided |
| 207 json_config = {} | 214 json_config = {} |
| 208 if args.json_conf != 'None' or '': | 215 if args.json_conf != 'None' or '': |
| 209 with open(args.json_conf, "r") as f: | 216 with open(args.json_conf, "r") as f: |