Mercurial > repos > goeckslab > scimap_phenotyping
comparison mcmicro_to_anndata.py @ 0:7ed4b55b11f7 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
| author | goeckslab |
|---|---|
| date | Tue, 19 Jul 2022 20:29:22 +0000 |
| parents | |
| children | ce22e846c5e4 |
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| -1:000000000000 | 0:7ed4b55b11f7 |
|---|---|
| 1 import argparse | |
| 2 import json | |
| 3 import warnings | |
| 4 | |
| 5 import scimap as sm | |
| 6 | |
| 7 | |
| 8 def main(inputs, outfile): | |
| 9 """ | |
| 10 Parameter | |
| 11 --------- | |
| 12 inputs : str | |
| 13 File path to galaxy tool parameter. | |
| 14 | |
| 15 outfile : str | |
| 16 File path to estimator. | |
| 17 """ | |
| 18 warnings.simplefilter('ignore') | |
| 19 | |
| 20 with open(inputs, 'r') as param_handler: | |
| 21 params = json.load(param_handler) | |
| 22 | |
| 23 image_path = params['image_path'] | |
| 24 drop_markers = params['drop_markers'] | |
| 25 if not drop_markers: | |
| 26 drop_markers = None | |
| 27 else: | |
| 28 drop_markers = [x.strip() for x in drop_markers.split(',')] | |
| 29 options = params['options'] | |
| 30 for k, v in options.items(): | |
| 31 if v == '': | |
| 32 options[k] = None | |
| 33 | |
| 34 adata = sm.pp.mcmicro_to_scimap(image_path, drop_markers=drop_markers, **options) | |
| 35 | |
| 36 adata.write(outfile) | |
| 37 | |
| 38 | |
| 39 if __name__ == '__main__': | |
| 40 aparser = argparse.ArgumentParser() | |
| 41 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) | |
| 42 aparser.add_argument("-e", "--outfile", dest="outfile", required=True) | |
| 43 args = aparser.parse_args() | |
| 44 | |
| 45 main(args.inputs, args.outfile) |