annotate scimap_spatial.py @ 0:199b5f278356 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea

import argparse
import json
import warnings

import scimap as sm
from anndata import read_h5ad


def main(inputs, anndata, output):
    """
    Parameter
    ---------
    inputs : str
        File path to galaxy tool parameter.
    anndata : str
        File path to anndata containing phenotyping info.
    output : str
        File path to output.
    """
    warnings.simplefilter('ignore')

    with open(inputs, 'r') as param_handler:
        params = json.load(param_handler)

    adata = read_h5ad(anndata)

    tool = params['analyses']['selected_tool']
    tool_func = getattr(sm.tl, tool)

    options = params['analyses']['options']
    if tool == 'cluster':
        options['method'] = params['analyses']['method']
        subset_genes = options.pop('subset_genes')
        if subset_genes:
            options['subset_genes'] = \
                [x.strip() for x in subset_genes.split(',')]
        sub_cluster_group = options.pop('sub_cluster_group')
        if sub_cluster_group:
            options['sub_cluster_group'] = \
                [x.strip() for x in sub_cluster_group.split(',')]

    for k, v in options.items():
        if v == '':
            options[k] = None

    tool_func(adata, **options)

    if tool == 'spatial_lda':
        adata.uns.pop('spatial_lda_model')

    adata.write(output)


if __name__ == '__main__':
    aparser = argparse.ArgumentParser()
    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
    aparser.add_argument("-e", "--output", dest="output", required=True)
    aparser.add_argument("-a", "--anndata", dest="anndata", required=True)

    args = aparser.parse_args()

    main(args.inputs, args.anndata, args.output)