comparison data_manager/kraken2_build_database.py @ 3:19b6a2f0dbe2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

2:edacc4bcd3cb

    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
    parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
    args = parser.parse_args()

    data_manager_input = json.loads(open(args.data_manager_json).read())

    target_directory = data_manager_input['output_data'][0]['extra_files_path']

    try:
        os.mkdir( target_directory )
    except OSError as exc:
        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
            pass
        else:
            raise

    data_manager_output = {}

            target_directory,
        )
    else:
        sys.exit("Invalid database type")

    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True))


if __name__ == "__main__":
    main()

3:19b6a2f0dbe2

    parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
    parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
    args = parser.parse_args()

    with open(args.data_manager_json) as fh:
        data_manager_input = json.load(fh)

    target_directory = data_manager_input['output_data'][0]['extra_files_path']

    try:
        os.mkdir(target_directory)
    except OSError as exc:
        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
            pass
        else:
            raise

    data_manager_output = {}

            target_directory,
        )
    else:
        sys.exit("Invalid database type")

    with open(args.data_manager_json, 'w') as fh:
        json.dump(data_manager_output, fh, sort_keys=True)


if __name__ == "__main__":
    main()