comparison data_manager/fetch_artic_primers.py @ 3:6114f017f819 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_refseq commit 120c6491f4b0888220e432693a9805d8198d7397"

2:119f459fc35f

    parser = argparse.ArgumentParser(description='Fetch ARTIC primer files for Galaxy use')
    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('--primers', default='ARTCIv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch')
    args = parser.parse_args()
    fetch_artic_primers(args.galaxy_datamanager_filename, args.output_directory, args.primers)

3:6114f017f819

    parser = argparse.ArgumentParser(description='Fetch ARTIC primer files for Galaxy use')
    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('--primers', default='ARTCIv1,ARTICv2,ARTICv3', action=SplitArgs, help='Comma separated list of primers to fetch')
    args = parser.parse_args()
    
    config = json.load(open(args.galaxy_datamanager_filename))
    output_directory = config.get('output_data', [{}])[0].get('extra_files_path', None)
    if output_directory is None:
        output_directory = args.output_directory
    fetch_artic_primers(args.galaxy_datamanager_filename, output_directory, args.primers)