Mercurial > repos > rliterman > csp2

comparison CSP2/bin/runSNPPipeline.py @ 28:893a6993efe3

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 13:48:13 -0500
parents 792274118b2e
children 93393808f415
comparison
equal deleted inserted replaced
27:792274118b2e 28:893a6993efe3
641 parser.add_argument('--min_iden', default=99,type=float, help='Minimum identity') 641 parser.add_argument('--min_iden', default=99,type=float, help='Minimum identity')
642 parser.add_argument('--ref_edge', default=150,type=int, help='Reference edge') 642 parser.add_argument('--ref_edge', default=150,type=int, help='Reference edge')
643 parser.add_argument('--query_edge', default=150,type=int, help='Query edge') 643 parser.add_argument('--query_edge', default=150,type=int, help='Query edge')
644 parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows') 644 parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows')
645 parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs') 645 parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs')
646 parser.add_argument('--trim_name', type=str, default="", help='trim name') 646 parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
647 parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing') 647 parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing')
648 parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory') 648 parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory')
649 parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)') 649 parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)')
650 args = parser.parse_args() 650 args = parser.parse_args()
651 651