Mercurial > repos > galaxytrakr > plasmidtrakr
changeset 2:954eccb7cc48 draft
planemo upload commit 8da69fa6fb55921a1b005486e59563f0c6956c2e
| author | galaxytrakr |
|---|---|
| date | Wed, 29 Apr 2026 16:33:55 +0000 |
| parents | fe9ff3859d68 |
| children | 6c88e978d6ad |
| files | predict_source.py |
| diffstat | 1 files changed, 2 insertions(+), 3 deletions(-) [+] |
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--- a/predict_source.py Wed Apr 29 15:26:26 2026 +0000 +++ b/predict_source.py Wed Apr 29 16:33:55 2026 +0000 @@ -10,11 +10,10 @@ def main(): parser = argparse.ArgumentParser(description="Predict the source of an isolate using a trained Random Forest model and Mash distances.") + parser.add_argument('--version', action='version', version='PlasmidTrakr v0.1.0') + parser.add_argument("-i", "--input", required=True, help="Input Mash screen/dist file for one or more isolates.") - - # --- KEY FIX 1: Replaced -m and -f with a single -b (bundle) argument --- parser.add_argument("-b", "--bundle", required=True, help="Path to the bundled model and features (.joblib file)") - parser.add_argument("-t", "--threshold", type=float, default=0.95, help="Mash identity threshold (default: 0.95)") parser.add_argument("-o", "--output", default="predictions.tsv", help="Output file for predictions (default: predictions.tsv)") args = parser.parse_args()