Mercurial > repos > galaxyp > fastg2protlib
comparison app_validate.py @ 0:6b226c5907a1 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
| author | galaxyp |
|---|---|
| date | Fri, 07 Aug 2020 06:17:31 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:6b226c5907a1 |
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| 1 import argparse | |
| 2 | |
| 3 import fastg2protlib.fastg2protlib as fg | |
| 4 | |
| 5 | |
| 6 if __name__ == "__main__": | |
| 7 parser = argparse.ArgumentParser(description="Run peptides for fastg") | |
| 8 parser.add_argument("msgf", help="Path MSGF+ tabular results.") | |
| 9 parser.add_argument( | |
| 10 "-d", | |
| 11 "--dbname", | |
| 12 default="results.db", | |
| 13 help="Name for the results database. Defaults to results.db", | |
| 14 ) | |
| 15 parser.add_argument( | |
| 16 "-f", | |
| 17 "--fdr", | |
| 18 default=0.10, | |
| 19 type=float, | |
| 20 help="FDR cutoff for accepting PSM validation.", | |
| 21 ) | |
| 22 parser.add_argument( | |
| 23 "-x", | |
| 24 "--decoy_header", | |
| 25 default="XXX_", | |
| 26 help="String used for marking decoy proteins.", | |
| 27 ) | |
| 28 | |
| 29 args = parser.parse_args() | |
| 30 fg.verified_proteins( | |
| 31 args.msgf, fdr_level=0.10, decoy_header="XXX_", db_name=args.dbname | |
| 32 ) |