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comparison unipept.py @ 8:7863f1abcdda draft

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planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
author galaxyp
date Sat, 02 Jul 2022 13:46:38 +0000
parents 75b3b3d0adbf
children
comparison
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7:75b3b3d0adbf 8:7863f1abcdda
484 parser.add_option('-I', '--ipr_tsv', dest='ipr_tsv', default=None, help='Output file path for InterPro TAB-separated-values (.tsv) formatted results') 484 parser.add_option('-I', '--ipr_tsv', dest='ipr_tsv', default=None, help='Output file path for InterPro TAB-separated-values (.tsv) formatted results')
485 parser.add_option('-L', '--lineage_tsv', dest='lineage_tsv', default=None, help='Output file path for Lineage TAB-separated-values (.tsv) formatted results') 485 parser.add_option('-L', '--lineage_tsv', dest='lineage_tsv', default=None, help='Output file path for Lineage TAB-separated-values (.tsv) formatted results')
486 parser.add_option('-T', '--tsv', dest='tsv', default=None, help='Output file path for TAB-separated-values (.tsv) formatted results') 486 parser.add_option('-T', '--tsv', dest='tsv', default=None, help='Output file path for TAB-separated-values (.tsv) formatted results')
487 parser.add_option('-C', '--csv', dest='csv', default=None, help='Output file path for Comma-separated-values (.csv) formatted results') 487 parser.add_option('-C', '--csv', dest='csv', default=None, help='Output file path for Comma-separated-values (.csv) formatted results')
488 parser.add_option('-U', '--unmatched', dest='unmatched', default=None, help='Output file path for peptide with no matches') 488 parser.add_option('-U', '--unmatched', dest='unmatched', default=None, help='Output file path for peptide with no matches')
489 parser.add_option('-u', '--url', dest='url', default='http://api.unipept.ugent.be/api/v1/', help='unipept url http://api.unipept.ugent.be/api/v1/') 489 parser.add_option('-u', '--url', dest='url', default='https://api.unipept.ugent.be/api/v1/', help='unipept url https://api.unipept.ugent.be/api/v1/')
490 parser.add_option('-P', '--peptide_match', dest='peptide_match', choices=['best', 'full', 'report'], default='best', help='Match whole peptide') 490 parser.add_option('-P', '--peptide_match', dest='peptide_match', choices=['best', 'full', 'report'], default='best', help='Match whole peptide')
491 parser.add_option('--unmatched_aa', dest='unmatched_aa', default=None, help='Show unmatched AA in peptide as') 491 parser.add_option('--unmatched_aa', dest='unmatched_aa', default=None, help='Show unmatched AA in peptide as')
492 # debug 492 # debug
493 parser.add_option('-g', '--get', dest='get', action='store_true', default=False, help='Use GET instead of POST') 493 parser.add_option('-g', '--get', dest='get', action='store_true', default=False, help='Use GET instead of POST')
494 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turning on debugging') 494 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turning on debugging')