comparison bismark_wrapper.py @ 16:a4504327c890 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"

15:0b656f8c5637

    parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format')
    parser.add_argument('--phred64-quals', dest='phred64', action="store_true")
    parser.add_argument('--non-directional', dest='non_directional', action="store_true")

    parser.add_argument('--skip-reads', dest='skip_reads', type=int)
    parser.add_argument('--qupto', type=int)

    # paired end options
    parser.add_argument('-I', '--minins', dest='min_insert')
    parser.add_argument('-X', '--maxins', dest='max_insert')

    parser.add_argument('--seed-extention-attempts', dest='seed_extention_attempts', type=int)
    # default 0
    parser.add_argument('--seed-mismatches', dest='seed_mismatches', type=int)
    # default 2
    parser.add_argument('--max-reseed', dest='max_reseed', type=int)
    """
    # default 70
    parser.add_argument( '--maqerr', dest='maqerr', type=int )
    """

    """
    The number of megabytes of memory a given thread is given to store path
    descriptors in --best mode. Best-first search must keep track of many paths
    at once to ensure it is always extending the path with the lowest cumulative

        cmd.append('--no-discordant')
    if args.no_mixed:
        cmd.append('--no-mixed')
    if args.skip_reads:
        cmd.extend(['--skip', str(args.skip_reads)])
    if args.qupto:
        cmd.extend(['--upto', 'args.qupto'])
    if args.phred64:
        cmd.append('--phred64-quals')
    if args.non_directional:

16:a4504327c890

    parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format')
    parser.add_argument('--phred64-quals', dest='phred64', action="store_true")
    parser.add_argument('--non-directional', dest='non_directional', action="store_true")

    parser.add_argument('--skip-reads', dest='skip_reads', type=int)
    parser.add_argument('--score-min', dest='score_min', type=str)
    parser.add_argument('--qupto', type=int)

    # paired end options
    parser.add_argument('-I', '--minins', dest='min_insert')
    parser.add_argument('-X', '--maxins', dest='max_insert')

    parser.add_argument('--seed-extention-attempts', dest='seed_extention_attempts', type=int)
    # default 0
    parser.add_argument('--seed-mismatches', dest='seed_mismatches', type=int)
    # default 2
    parser.add_argument('--max-reseed', dest='max_reseed', type=int)


    """
    The number of megabytes of memory a given thread is given to store path
    descriptors in --best mode. Best-first search must keep track of many paths
    at once to ensure it is always extending the path with the lowest cumulative

        cmd.append('--no-discordant')
    if args.no_mixed:
        cmd.append('--no-mixed')
    if args.skip_reads:
        cmd.extend(['--skip', str(args.skip_reads)])
    if args.score_min:
        cmd.extend(['--score_min', str(args.score_min)])
    if args.qupto:
        cmd.extend(['--upto', 'args.qupto'])
    if args.phred64:
        cmd.append('--phred64-quals')
    if args.non_directional: