comparison spectrast_params.py @ 5:274fdc50169b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty

4:c9bfe6adb7cd

                    ' to create an updated search.params')
    parser.add_argument(
        'param_files', nargs='*',
        help='A SpectraST search.params files')
    parser.add_argument(
        '-m', '--mode', choices=['search','create','filter'],
        help='')
    parser.add_argument(
        '-o', '--output',
        help='Output file  (-) for stdout')
    args = parser.parse_args()

    output_wtr = open(args.output, 'w')\
        if args.output and args.output != '-' else sys.stdout

    optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')

    valid_opts = search_opts if args.mode == 'search' else create_opts if args.mode == 'create' else filter_opts
    valid_params = dict()

    # Collect all valid_params
    def parse_params(param_file, fh, valid_opts):
        for i, line in enumerate(fh):

            print('parse_params: %s' % e, file=sys.stderr)

    # Write valid_params
    for valid_opt in valid_opts:
        if valid_opt in valid_params:
            print('%s = %s' % (valid_opt, valid_params[valid_opt]), file=output_wtr)


if __name__ == "__main__":
    __main__()

5:274fdc50169b

                    ' to create an updated search.params')
    parser.add_argument(
        'param_files', nargs='*',
        help='A SpectraST search.params files')
    parser.add_argument(
        '-m', '--mode', choices=['search', 'create', 'filter'],
        help='')
    parser.add_argument(
        '-o', '--output',
        help='Output file  (-) for stdout')
    args = parser.parse_args()

    output_wtr = open(args.output, 'w')\
        if args.output and args.output != '-' else sys.stdout

    optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')

    valid_opts = search_opts if args.mode == 'search'\
        else create_opts if args.mode == 'create' else filter_opts
    valid_params = dict()

    # Collect all valid_params
    def parse_params(param_file, fh, valid_opts):
        for i, line in enumerate(fh):

            print('parse_params: %s' % e, file=sys.stderr)

    # Write valid_params
    for valid_opt in valid_opts:
        if valid_opt in valid_params:
            print('%s = %s' % (valid_opt, valid_params[valid_opt]),
                  file=output_wtr)


if __name__ == "__main__":
    __main__()