Mercurial > repos > goeckslab > vitessce_spatial

comparison gate_finder.py @ 5:97be83fc3677 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 90f081e58b5ee41bba3a7e6f01d97b5bd9392759
author goeckslab
date Wed, 28 May 2025 21:14:59 +0000
parents 068da7f7cd83
children
comparison
equal deleted inserted replaced
4:068da7f7cd83 5:97be83fc3677
51 gate = np.mean(gmm.means_) 51 gate = np.mean(gmm.means_)
52 52
53 return get_gate_phenotype(gate, np.ravel(data_norm)) 53 return get_gate_phenotype(gate, np.ravel(data_norm))
54 54
55 55
56 def main(inputs, output, image, anndata, offsets=None, masks=None): 56 def main(inputs, output, image, anndata, offsets=None, masks=None, config_path=None):
57 """ 57 """
58 Parameter 58 Parameter
59 --------- 59 ---------
60 inputs : str 60 inputs : str
61 File path to galaxy tool parameter. 61 File path to galaxy tool parameter.
65 File path to the OME Tiff image. 65 File path to the OME Tiff image.
66 anndata : str 66 anndata : str
67 File path to anndata containing phenotyping info. 67 File path to anndata containing phenotyping info.
68 masks : str 68 masks : str
69 File path to the image masks. 69 File path to the image masks.
70 config_path : str
71 File path to the config containing galaxy_url and dataset_id.
70 """ 72 """
71 warnings.simplefilter('ignore') 73 warnings.simplefilter('ignore')
72 74
73 with open(inputs, 'r') as param_handler: 75 with open(inputs, 'r') as param_handler:
74 params = json.load(param_handler) 76 params = json.load(param_handler)
77
78 with open(config_path) as conf_fh:
79 config = json.load(conf_fh)
75 80
76 marker = params['marker'].strip() 81 marker = params['marker'].strip()
77 from_gate = params['from_gate'] 82 from_gate = params['from_gate']
78 to_gate = params['to_gate'] 83 to_gate = params['to_gate']
79 increment = params['increment'] 84 increment = params['increment']
80 x_coordinate = params['x_coordinate'].strip() or 'X_centroid' 85 x_coordinate = params['x_coordinate'].strip() or 'X_centroid'
81 y_coordinate = params['y_coordinate'].strip() or 'Y_centroid' 86 y_coordinate = params['y_coordinate'].strip() or 'Y_centroid'
87
88 galaxy_url = config["galaxy_url"]
89 dataset_id = config["dataset_id"]
90
91 # Build the prefix that Vitessce should use
92 display_prefix = (f"{galaxy_url}/api/datasets/{dataset_id}/display?filename=")
82 93
83 adata = read_h5ad(anndata) 94 adata = read_h5ad(anndata)
84 95
85 # If no raw data is available make a copy 96 # If no raw data is available make a copy
86 if adata.raw is None: 97 if adata.raw is None:
189 | (cell_set_sizes / lc) 200 | (cell_set_sizes / lc)
190 | (spatial) 201 | (spatial)
191 ) 202 )
192 203
193 # export config file 204 # export config file
194 config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output) 205 config_dict = vc.export(to='files', base_url=display_prefix, out_dir=output)
195 206
196 with open(Path(output).joinpath('config.json'), 'w') as f: 207 with open(Path(output).joinpath('config.json'), 'w') as f:
197 json.dump(config_dict, f, indent=4) 208 json.dump(config_dict, f, indent=4)
198 209
199 210
203 aparser.add_argument("-e", "--output", dest="output", required=True) 214 aparser.add_argument("-e", "--output", dest="output", required=True)
204 aparser.add_argument("-g", "--image", dest="image", required=True) 215 aparser.add_argument("-g", "--image", dest="image", required=True)
205 aparser.add_argument("-a", "--anndata", dest="anndata", required=True) 216 aparser.add_argument("-a", "--anndata", dest="anndata", required=True)
206 aparser.add_argument("-f", "--offsets", dest="offsets", required=False) 217 aparser.add_argument("-f", "--offsets", dest="offsets", required=False)
207 aparser.add_argument("-m", "--masks", dest="masks", required=False) 218 aparser.add_argument("-m", "--masks", dest="masks", required=False)
219 aparser.add_argument("--galaxy_config", dest="config_path", required=True)
208 220
209 args = aparser.parse_args() 221 args = aparser.parse_args()
210 222
211 main(args.inputs, args.output, args.image, args.anndata, args.offsets, args.masks) 223 main(args.inputs, args.output, args.image, args.anndata, args.offsets, args.masks, args.config_path)