--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scimap_spatial.py	Tue Jul 19 20:29:59 2022 +0000
@@ -0,0 +1,59 @@
+import argparse
+import json
+import warnings
+
+import scimap as sm
+from anndata import read_h5ad
+
+
+def main(inputs, anndata, output):
+    """
+    Parameter
+    ---------
+    inputs : str
+        File path to galaxy tool parameter.
+    anndata : str
+        File path to anndata containing phenotyping info.
+    output : str
+        File path to output.
+    """
+    warnings.simplefilter('ignore')
+
+    with open(inputs, 'r') as param_handler:
+        params = json.load(param_handler)
+
+    adata = read_h5ad(anndata)
+
+    tool = params['analyses']['selected_tool']
+    tool_func = getattr(sm.tl, tool)
+
+    options = params['analyses']['options']
+    if tool == 'cluster':
+        options['method'] = params['analyses']['method']
+        subset_genes = options.pop('subset_genes')
+        if subset_genes:
+            options['subset_genes'] = \
+                [x.strip() for x in subset_genes.split(',')]
+        sub_cluster_group = options.pop('sub_cluster_group')
+        if sub_cluster_group:
+            options['sub_cluster_group'] = \
+                [x.strip() for x in sub_cluster_group.split(',')]
+
+    for k, v in options.items():
+        if v == '':
+            options[k] = None
+
+    tool_func(adata, **options)
+
+    adata.write(output)
+
+
+if __name__ == '__main__':
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument("-e", "--output", dest="output", required=True)
+    aparser.add_argument("-a", "--anndata", dest="anndata", required=True)
+
+    args = aparser.parse_args()
+
+    main(args.inputs, args.anndata, args.output)