Mercurial > repos > goeckslab > scimap_spatial

annotate mcmicro_to_anndata.py @ 5:d9f414be2f09 draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
author goeckslab
date Wed, 11 Jun 2025 22:18:44 +0000
parents d19c068c2490
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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diff changeset
1 import argparse
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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2 import json
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3 import warnings
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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goeckslab
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5 import scimap as sm
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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8 def main(inputs, outfile):
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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9 """
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goeckslab
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10 Parameter
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11 ---------
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12 inputs : str
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goeckslab
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13 File path to galaxy tool parameter.
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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15 outfile : str
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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16 File path to estimator.
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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17 """
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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18 warnings.simplefilter('ignore')
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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20 with open(inputs, 'r') as param_handler:
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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21 params = json.load(param_handler)
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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22
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d9f414be2f09 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
goeckslab
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23 image_path = params['image_path']['source_path']
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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24 drop_markers = params['drop_markers']
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25 if not drop_markers:
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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26 drop_markers = None
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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27 else:
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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28 drop_markers = [x.strip() for x in drop_markers.split(',')]
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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29 options = params['options']
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d9f414be2f09 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
goeckslab
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30 if not options.get('custom_imageid'):
d9f414be2f09 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
goeckslab
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31 element_identifier = params['image_path']['element_identifier']
d9f414be2f09 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
goeckslab
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32 # Might be a list on unpatched versions of Galaxy, xref: https://github.com/galaxyproject/galaxy/pull/20438
d9f414be2f09 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
goeckslab
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33 options['custom_imageid'] = element_identifier if isinstance(element_identifier, str) else element_identifier[0]
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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34 for k, v in options.items():
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goeckslab
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35 if v == '':
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
goeckslab
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36 options[k] = None
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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37
2
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goeckslab
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38 adata = sm.pp.mcmicro_to_scimap(
d19c068c2490 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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39 image_path,
d19c068c2490 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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40 drop_markers=drop_markers,
d19c068c2490 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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41 **options
d19c068c2490 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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42 )
0
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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44 adata.write(outfile)
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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47 if __name__ == '__main__':
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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48 aparser = argparse.ArgumentParser()
42e6c251bfd0 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
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49 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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50 aparser.add_argument("-e", "--outfile", dest="outfile", required=True)
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51 args = aparser.parse_args()
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52
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53 main(args.inputs, args.outfile)