comparison msmetaenhancer_wrapper.py @ 3:f387ebd6b734 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"

2:8338640d8676

    parser = argparse.ArgumentParser(description="Annotate MSP file.")
    parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
    parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
    parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
    args = parser.parse_args()

    app = Application(log_file=args.log_file)

    # set matchms logging level to avoid extensive messages in stdout while reading file
    set_matchms_logger_level("ERROR")
    # import .msp file
    app.load_spectra(args.input_file, file_format='msp')

3:f387ebd6b734

    parser = argparse.ArgumentParser(description="Annotate MSP file.")
    parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
    parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
    parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
    parser.add_argument("--log_level", type=str, default='info',
                        help="Severity of log messages  present in the log file.")
    args = parser.parse_args()

    app = Application(log_level=args.log_level, log_file=args.log_file)

    # set matchms logging level to avoid extensive messages in stdout while reading file
    set_matchms_logger_level("ERROR")
    # import .msp file
    app.load_spectra(args.input_file, file_format='msp')