comparison data_manager/fetch_refseq.py @ 11:b1e8f8a613e6 draft

planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty

10:d878e492546c

    parser = argparse.ArgumentParser(description='Download RefSeq databases')
    parser.add_argument('--debug', default=False, action='store_true', help='Print debugging output to stderr (verbose)')
    parser.add_argument('--compress', default=False, action='store_true', help='Compress output files')
    parser.add_argument('--output_directory', default='tmp', help='Directory to write output to')
    parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs')
    parser.add_argument('--division_names', nargs='+', help='RefSeq divisions to download')
    parser.add_argument('--mol_types', nargs='+', help='Molecule types (genomic, rna, protein) to fetch')
    parser.add_argument('--pin_date', help='Force download date to this version string')
    args = parser.parse_args()
    
    division_names = args.division_names.split(',')
    mol_types = args.mol_types.split(',')
    if args.galaxy_datamanager_filename is not None:
        dm_opts = json.loads(open(args.galaxy_datamanager_filename).read())
        output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter

11:b1e8f8a613e6

    parser = argparse.ArgumentParser(description='Download RefSeq databases')
    parser.add_argument('--debug', default=False, action='store_true', help='Print debugging output to stderr (verbose)')
    parser.add_argument('--compress', default=False, action='store_true', help='Compress output files')
    parser.add_argument('--output_directory', default='tmp', help='Directory to write output to')
    parser.add_argument('--galaxy_datamanager_filename', help='Galaxy JSON format file describing data manager inputs')
    parser.add_argument('--division_names', help='RefSeq divisions to download')
    parser.add_argument('--mol_types', help='Molecule types (genomic, rna, protein) to fetch')
    parser.add_argument('--pin_date', help='Force download date to this version string')
    args = parser.parse_args()

    division_names = args.division_names.split(',')
    mol_types = args.mol_types.split(',')
    if args.galaxy_datamanager_filename is not None:
        dm_opts = json.loads(open(args.galaxy_datamanager_filename).read())
        output_directory = dm_opts['output_data'][0]['extra_files_path'] # take the extra_files_path of the first output parameter