Mercurial > repos > galaxyp > psm_validation
diff application.py @ 0:ddcab0f11473 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
author | galaxyp |
---|---|
date | Thu, 15 Oct 2020 07:45:17 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/application.py Thu Oct 15 07:45:17 2020 +0000 @@ -0,0 +1,66 @@ +import argparse + +import psmfragmentation.psmfragmentation as pf + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Run PSM Validator") + parser.add_argument( + "-d", + "--dbname", + help="Path to mzsqlite db", + ) + parser.add_argument( + "-p", + "--peptides", + help="Path to peptide sequence file", + ) + parser.add_argument( + "-n", + "--neutral", + action="store_true", + default=False, + help="Calculate netutral loss", + ) + parser.add_argument( + "-i", + "--internal", + action="store_true", + default=False, + help="Calculate internals", + ) + parser.add_argument( + "-e", "--epsilon", type=float + ) + parser.add_argument( + "-b", + "--b_run", + type=int, + default=2, + help="Number of consecutive b-ions" + ) + parser.add_argument( + "-y", + "--y_run", + type=int, + default=2, + help="Number of consecutive y-ions" + ) + + parser.add_argument( + "-t", + "--test", + action="store_true", + default=False + ) + + args = parser.parse_args() + + itypes = ['b', 'y'] + if args.neutral: + itypes.extend(['b-H2O', 'b-NH3', 'y-H2O', 'y-NH3']) + + if args.internal: + itypes.append('M') + + pf.score_psms(args.dbname, args.peptides, ion_types=itypes, epsilon=args.epsilon, maxcharge=1, b_run=args.b_run, y_run=args.y_run, a_test=args.test)