Mercurial > repos > goeckslab > gate_finder
diff gate_finder.py @ 5:e860ca30cd0b draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 90f081e58b5ee41bba3a7e6f01d97b5bd9392759
author | goeckslab |
---|---|
date | Wed, 28 May 2025 21:14:52 +0000 |
parents | 5f4a4dd06bc9 |
children |
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--- a/gate_finder.py Thu Feb 20 19:47:28 2025 +0000 +++ b/gate_finder.py Wed May 28 21:14:52 2025 +0000 @@ -53,7 +53,7 @@ return get_gate_phenotype(gate, np.ravel(data_norm)) -def main(inputs, output, image, anndata, offsets=None, masks=None): +def main(inputs, output, image, anndata, offsets=None, masks=None, config_path=None): """ Parameter --------- @@ -67,12 +67,17 @@ File path to anndata containing phenotyping info. masks : str File path to the image masks. + config_path : str + File path to the config containing galaxy_url and dataset_id. """ warnings.simplefilter('ignore') with open(inputs, 'r') as param_handler: params = json.load(param_handler) + with open(config_path) as conf_fh: + config = json.load(conf_fh) + marker = params['marker'].strip() from_gate = params['from_gate'] to_gate = params['to_gate'] @@ -80,6 +85,12 @@ x_coordinate = params['x_coordinate'].strip() or 'X_centroid' y_coordinate = params['y_coordinate'].strip() or 'Y_centroid' + galaxy_url = config["galaxy_url"] + dataset_id = config["dataset_id"] + + # Build the prefix that Vitessce should use + display_prefix = (f"{galaxy_url}/api/datasets/{dataset_id}/display?filename=") + adata = read_h5ad(anndata) # If no raw data is available make a copy @@ -191,7 +202,7 @@ ) # export config file - config_dict = vc.export(to='files', base_url='http://localhost', out_dir=output) + config_dict = vc.export(to='files', base_url=display_prefix, out_dir=output) with open(Path(output).joinpath('config.json'), 'w') as f: json.dump(config_dict, f, indent=4) @@ -205,7 +216,8 @@ aparser.add_argument("-a", "--anndata", dest="anndata", required=True) aparser.add_argument("-f", "--offsets", dest="offsets", required=False) aparser.add_argument("-m", "--masks", dest="masks", required=False) + aparser.add_argument("--galaxy_config", dest="config_path", required=True) args = aparser.parse_args() - main(args.inputs, args.output, args.image, args.anndata, args.offsets, args.masks) + main(args.inputs, args.output, args.image, args.anndata, args.offsets, args.masks, args.config_path)