diff scale_cell_coordinates.py @ 5:afa3cb2110eb draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scale_cell_coordinates.py	Thu Jul 11 22:41:26 2024 +0000
@@ -0,0 +1,50 @@
+import argparse
+import json
+import warnings
+
+import anndata as ad
+
+
+def main(inputs, output):
+
+    """
+    inputs : str
+        File path to galaxy tool JSON inputs config file
+    output: str
+        File path to save the output h5ad file
+    """
+    warnings.simplefilter('ignore')
+
+    # read inputs JSON
+    with open(inputs, 'r') as param_handler:
+        params = json.load(param_handler)
+
+    # read input anndata file
+    adata = ad.read_h5ad(params['anndata'])
+
+    # scale coords
+    unit = params['unit']
+    new_col_names = []
+    for c in [params['x_coord'], params['y_coord']]:
+        scaled_col_name = f'{c}_{unit}'
+        adata.obs[scaled_col_name] = adata.obs[c] * params['resolution']
+        new_col_names.append(scaled_col_name)
+
+    # overwrite adata.obsm['spatial'] with scaled coordinates
+    adata.obsm['spatial'] = adata.obs[scaled_col_name].values
+
+    # write out anndata to h5ad file
+    adata.write_h5ad(output)
+
+
+if __name__ == '__main__':
+
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument(
+        "-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument(
+        "-o", "--output", dest="output", required=False)
+
+    args = aparser.parse_args()
+
+    main(args.inputs, args.output)