comparison iedb_api.py @ 1:6cf84410cb2e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"

0:fe3c43451319

prediction_methods = {'mhci': mhci_methods,
                      'mhcii': mhcii_methods,
                      'processing': processing_methods,
                      'mhcnp': mhcnp_methods,
                      'bcell': bcell_methods}
all_methods = set(mhci_methods + mhcii_methods +
                  mhcnp_methods + bcell_methods)
prediction_lengths = {'mhci': range(8, 16),
                      'mhcii': range(11, 31),
                      'processing': range(8, 15),
                      'mhcnp': range(8, 12),
                      'bcell': range(8, 16)}

                        default=None,
                        help='File of HLA alleles')
    parser.add_argument('-l', '--length',
                        action="append",
                        default=[],
                        help='lengths for which to make predictions, ' +
                             '1 per allele')
    parser.add_argument('-w', '--window_size',
                        type=int,
                        default=None,
                        help='window_size for bcell prediction')
    parser.add_argument('-i', '--input',
                        default=None,
                        help='Input file for peptide sequences ' +
                             '(fasta or tabular)')
    parser.add_argument('-c', '--column',
                        default=None,
                        help='Peptide Column in a tabular input file')
    parser.add_argument('-C', '--id_column',

    if args.prediction != 'bcell':
        if not args.allele and not args.allelefile:
            warn_err('-a allele or -A allelefile required\n', exit_code=1)

    if not (args.sequence or args.input):
        warn_err('NO Sequences given: ' +
                 'either -s sequence or -i input_file is required\n',
                 exit_code=1)

    if args.output is not None:
        try:

1:6cf84410cb2e

prediction_methods = {'mhci': mhci_methods,
                      'mhcii': mhcii_methods,
                      'processing': processing_methods,
                      'mhcnp': mhcnp_methods,
                      'bcell': bcell_methods}
all_methods = set(mhci_methods + mhcii_methods + mhcnp_methods + bcell_methods)
prediction_lengths = {'mhci': range(8, 16),
                      'mhcii': range(11, 31),
                      'processing': range(8, 15),
                      'mhcnp': range(8, 12),
                      'bcell': range(8, 16)}

                        default=None,
                        help='File of HLA alleles')
    parser.add_argument('-l', '--length',
                        action="append",
                        default=[],
                        help='lengths for which to make predictions, '
                             '1 per allele')
    parser.add_argument('-w', '--window_size',
                        type=int,
                        default=None,
                        help='window_size for bcell prediction')
    parser.add_argument('-i', '--input',
                        default=None,
                        help='Input file for peptide sequences '
                             '(fasta or tabular)')
    parser.add_argument('-c', '--column',
                        default=None,
                        help='Peptide Column in a tabular input file')
    parser.add_argument('-C', '--id_column',

    if args.prediction != 'bcell':
        if not args.allele and not args.allelefile:
            warn_err('-a allele or -A allelefile required\n', exit_code=1)

    if not (args.sequence or args.input):
        warn_err('NO Sequences given: '
                 'either -s sequence or -i input_file is required\n',
                 exit_code=1)

    if args.output is not None:
        try: