annotate ipapy2_clustering.py @ 0:428abc41a101 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 CustomArgumentParser


def main(input_dataset, Cthr, RTwin, Intmode, output_dataset):
    write_func, file_path = output_dataset
    clustered_df = ipa.clusterFeatures(
        input_dataset, Cthr=Cthr, RTwin=RTwin, Intmode=Intmode
    )
    write_func(clustered_df, file_path)


if __name__ == "__main__":
    parser = CustomArgumentParser(
        description=" Clustering MS1 features based on correlation across samples."
    )
    parser.add_argument(
        "--input_dataset",
        nargs=2,
        action="load_data",
        required=True,
        help="The unclustered MS1 intensities file path.",
    )

    parser.add_argument(
        "--Cthr",
        type=float,
        default=0.8,
        help="Minimum correlation allowed in each cluster. Default value 0.8.",
    )

    parser.add_argument(
        "--RTwin",
        type=float,
        default=1,
        help=(
            "Maximum difference in RT time between features in the same cluster."
            " Default value 1."
        ),
    )

    parser.add_argument(
        "--Intmode",
        type=str,
        default="max",
        choices=["max", "ave"],
        help="intensity mode. Default 'max' or 'ave'.",
    )
    args = parser.parse_args()
    main(args.input_dataset, args.Cthr, args.RTwin, args.Intmode, args.output_dataset)