scimap_mcmicro_to_anndata: scimap

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5

comparison

equal deleted inserted replaced

--1:000000000000
+:2a3152751ca8
+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)
+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)

Mercurial > repos > goeckslab > scimap_mcmicro_to_anndata