comparison data_manager/funannotate.py @ 2:28fc15925666 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"

1:1a0230433e1a

if __name__ == "__main__":

    parser = argparse.ArgumentParser()
    parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
    parser.add_argument("version_id")
    parser.add_argument("datatable_name")
    parser.add_argument("galaxy_datamanager_filename")
    args = parser.parse_args()

    os.mkdir(output_directory)
    cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
    if args.partial:
        cmd_args += ['-i', 'merops', '-b', 'eukaryota']
    proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
    return_code = proc.wait()
    if return_code:
        print("Error downloading Funannotate database.", file=sys.stderr)
        sys.exit(return_code)

2:28fc15925666

if __name__ == "__main__":

    parser = argparse.ArgumentParser()
    parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
    parser.add_argument('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)')
    parser.add_argument("version_id")
    parser.add_argument("datatable_name")
    parser.add_argument("galaxy_datamanager_filename")
    args = parser.parse_args()

    os.mkdir(output_directory)
    cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
    if args.partial:
        cmd_args += ['-i', 'merops', '-b', 'eukaryota']
    if args.wget:
        cmd_args += ['--wget']
    proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
    return_code = proc.wait()
    if return_code:
        print("Error downloading Funannotate database.", file=sys.stderr)
        sys.exit(return_code)