--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anndata_to_csv.py	Mon Jun 10 18:45:21 2024 +0000
@@ -0,0 +1,45 @@
+import argparse
+import json
+import warnings
+
+import scimap as sm
+from anndata import read_h5ad
+
+
+def main(inputs, outfile):
+    """
+    Parameters
+    ---------
+    inputs : str
+        File path to galaxy tool parameter.
+    anndata : str
+        File path to anndata.
+    output : str
+        File path to output.
+    """
+    warnings.simplefilter('ignore')
+
+    with open(inputs, 'r') as param_handler:
+        params = json.load(param_handler)
+
+    adata = read_h5ad(params['anndata'])
+
+    if params['layer'] == 'x':
+        params['layer'] = None
+
+    df = sm.hl.scimap_to_csv(
+        adata=adata,
+        layer=params['layer'],
+        CellID=params['cellid'],
+    )
+
+    df.to_csv(outfile, index=False)
+
+
+if __name__ == '__main__':
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument("-e", "--outfile", dest="outfile", required=True)
+    args = aparser.parse_args()
+
+    main(args.inputs, args.outfile)