Mercurial > repos > goeckslab > scimap_anndata_to_csv

annotate scimap_plotting.py @ 2:302ddf03402f draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
author goeckslab
date Tue, 30 Jul 2024 18:21:02 +0000
parents 199b5f278356
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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diff changeset
1 import argparse
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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2 import json
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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3 import os
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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4 import warnings
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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5
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302ddf03402f planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
goeckslab
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6 import matplotlib.pyplot as plt
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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7 import numpy as np
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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8 import scimap as sm
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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9 import seaborn as sns
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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10 from anndata import read_h5ad
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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12 sns.set(color_codes=True)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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15 def main(inputs, anndata, output):
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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16 """
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17 Parameter
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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18 ---------
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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19 inputs : str
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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20 File path to galaxy tool parameter.
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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21 anndata : str
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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22 File path to anndata containing phenotyping info.
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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23 output : str
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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24 File path to output.
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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25 """
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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26 warnings.simplefilter('ignore')
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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28 with open(inputs, 'r') as param_handler:
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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29 params = json.load(param_handler)
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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31 adata = read_h5ad(anndata)
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33 tool = params['analyses']['selected_tool']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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34 options = params['analyses']['options']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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36 if tool == 'stacked_barplot':
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
goeckslab
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38 # parse list text arguments
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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39 for o in options.copy():
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40 opt = options.pop(o)
302ddf03402f planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
goeckslab
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41 if o == 'matplotlib_cmap':
302ddf03402f planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
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42 matplotlib_cmap = opt
302ddf03402f planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
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43 elif opt != "":
302ddf03402f planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit c39cea5ae2ebf61b3d51d687fd9d2930c907b72d
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44 options[o] = [x.strip() for x in opt.split(',')]
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199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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46 # add base args into options dict to pass to tool
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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47 options['x_axis'] = params['analyses']['x_axis']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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48 options['y_axis'] = params['analyses']['y_axis']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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49 options['method'] = params['analyses']['method']
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51 options['return_data'] = True
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53 df = sm.pl.stacked_barplot(adata, **options)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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54
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55 # Plotting
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56 sns.set_theme(style="white")
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57 ax = df.plot.bar(stacked=True, cmap=matplotlib_cmap)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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58 fig = ax.get_figure()
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59 handles, labels = ax.get_legend_handles_labels()
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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60 ax.legend(
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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61 reversed(handles),
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62 reversed(labels),
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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63 bbox_to_anchor=(1, 1),
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64 loc='upper left'
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65 )
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66 plt.tight_layout()
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67
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68 # # save and close
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69 fig.savefig('out.png', dpi=300)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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70 plt.close(fig)
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72 if tool == 'voronoi':
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73
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74 plt.style.use('fast')
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76 tool_func = getattr(sm.pl, tool)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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77
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78 # x_lim/y_lim need to be parsed from comma-sep str to integer tuples
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79 for lim in ['x_lim', 'y_lim']:
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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80 opt_list = options.pop(lim)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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81 if opt_list:
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82 options[lim] = [int(x.strip()) for x in opt_list.split(',')]
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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83
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84 # parse list text arguments
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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85 for cat in ['overlay_points_categories', 'overlay_drop_categories']:
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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86 opt_list = options.pop(cat)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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87 if opt_list:
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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88 options[cat] = [x.strip() for x in opt_list.split(',')]
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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89
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90 # add base args into options dict to pass to tool
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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91 options['color_by'] = params['analyses']['color_by']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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92 options['x_coordinate'] = params['analyses']['x_coordinate']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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93 options['y_coordinate'] = params['analyses']['y_coordinate']
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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94
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95 # fill any missing params with None as tool expects
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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96 for k, v in options.items():
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97 if v == '':
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98 options[k] = None
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99
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100 options['saveDir'] = os.getcwd()
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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101 options['fileName'] = 'out.png'
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102
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103 if options['size_max'] is None:
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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104 options['size_max'] = np.inf
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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105
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goeckslab
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106 # call the tool and unpack all options
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107 tool_func(adata, **options)
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108
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109
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110 if __name__ == '__main__':
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111 aparser = argparse.ArgumentParser()
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112 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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113 aparser.add_argument("-a", "--anndata", dest="anndata", required=True)
199b5f278356 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
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114 aparser.add_argument("-e", "--output", dest="output", required=True)
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115
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116 args = aparser.parse_args()
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117
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118 main(args.inputs, args.anndata, args.output)