annotate scimap_spatial.py @ 0:7ed4b55b11f7 draft

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

1 import argparse
2 import json
3 import warnings
4 
5 import scimap as sm
6 from anndata import read_h5ad
7 
8 
9 def main(inputs, anndata, output):
10     """
11     Parameter
12     ---------
13     inputs : str
14         File path to galaxy tool parameter.
15     anndata : str
16         File path to anndata containing phenotyping info.
17     output : str
18         File path to output.
19     """
20     warnings.simplefilter('ignore')
21 
22     with open(inputs, 'r') as param_handler:
23         params = json.load(param_handler)
24 
25     adata = read_h5ad(anndata)
26 
27     tool = params['analyses']['selected_tool']
28     tool_func = getattr(sm.tl, tool)
29 
30     options = params['analyses']['options']
31     if tool == 'cluster':
32         options['method'] = params['analyses']['method']
33         subset_genes = options.pop('subset_genes')
34         if subset_genes:
35             options['subset_genes'] = \
36                 [x.strip() for x in subset_genes.split(',')]
37         sub_cluster_group = options.pop('sub_cluster_group')
38         if sub_cluster_group:
39             options['sub_cluster_group'] = \
40                 [x.strip() for x in sub_cluster_group.split(',')]
41 
42     for k, v in options.items():
43         if v == '':
44             options[k] = None
45 
46     tool_func(adata, **options)
47 
48     adata.write(output)
49 
50 
51 if __name__ == '__main__':
52     aparser = argparse.ArgumentParser()
53     aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
54     aparser.add_argument("-e", "--output", dest="output", required=True)
55     aparser.add_argument("-a", "--anndata", dest="anndata", required=True)
56 
57     args = aparser.parse_args()
58 
59     main(args.inputs, args.anndata, args.output)