Mercurial > repos > goeckslab > scimap_phenotyping

comparison mcmicro_to_anndata.py @ 2:ce22e846c5e4 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:44:25 +0000
parents 7ed4b55b11f7
children
comparison
equal deleted inserted replaced
1:dcfcad35e847 2:ce22e846c5e4
29 options = params['options'] 29 options = params['options']
30 for k, v in options.items(): 30 for k, v in options.items():
31 if v == '': 31 if v == '':
32 options[k] = None 32 options[k] = None
33 33
34 adata = sm.pp.mcmicro_to_scimap(image_path, drop_markers=drop_markers, **options) 34 adata = sm.pp.mcmicro_to_scimap(
35 image_path,
36 drop_markers=drop_markers,
37 **options
38 )
35 39
36 adata.write(outfile) 40 adata.write(outfile)
37 41
38 42
39 if __name__ == '__main__': 43 if __name__ == '__main__':