annotate ipapy2_MS1_annotation.py @ 0:cb18b8fcb441 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a

from ipaPy2 import ipa
from utils import flattern_annotations, MSArgumentParser


def main(
    input_dataset_database,
    input_dataset_adduct,
    ppm,
    ratiosd,
    ppmunk,
    ratiounk,
    ppmthr,
    pRTNone,
    pRTout,
    output_dataset,
    ncores,
):
    write_func, file_path = output_dataset

    annotations = ipa.MS1annotation(
        input_dataset_database,
        input_dataset_adduct,
        ppm=ppm,
        ratiosd=ratiosd,
        ppmunk=ppmunk,
        ratiounk=ratiounk,
        ppmthr=ppmthr,
        pRTNone=pRTNone,
        pRTout=pRTout,
        ncores=ncores,
    )
    annotations_flat = flattern_annotations(annotations)
    write_func(annotations_flat, file_path)


if __name__ == "__main__":
    parser = MSArgumentParser("""
    Annotation of the dataset based on the MS1 information. Prior probabilities
        are based on mass only, while post probabilities are based on mass, RT,
        previous knowledge and isotope patterns.
    """)
    parser.add_argument(
        "--input_dataset_database",
        nargs=2,
        action="load_data",
        required=True,
        help=(
            "A dataset containing the MS1 data. Ideally obtained from"
            " map_isotope_patterns"
        ),
    )
    parser.add_argument(
        "--input_dataset_adducts",
        nargs=2,
        action="load_data",
        required=True,
        help="A dataset containing information on all possible adducts.",
    )

    args = parser.parse_args()
    main(
        args.input_dataset_database,
        args.input_dataset_adducts,
        args.ppm,
        args.ratiosd,
        args.ppmunk,
        args.ratiounk,
        args.ppmthr,
        args.pRTNone,
        args.pRTout,
        args.output_dataset,
        args.ncores,
    )