diff decoupler_pseudobulk.py @ 2:130e25d3ce92 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85a3118a571246d88aaad26733d0c62009cb736b

--- a/decoupler_pseudobulk.py	Wed Sep 27 01:11:32 2023 +0000
+++ b/decoupler_pseudobulk.py	Fri Oct 13 15:19:51 2023 +0000
@@ -165,9 +165,11 @@
 
     # Merge adata.obs fields specified in args.adata_obs_fields_to_merge
     if args.adata_obs_fields_to_merge:
-        fields = args.adata_obs_fields_to_merge.split(",")
-        check_fields(fields, adata)
-        adata = merge_adata_obs_fields(fields, adata)
+        # first split potential groups by ":" and iterate over them
+        for group in args.adata_obs_fields_to_merge.split(":"):
+            fields = group.split(",")
+            check_fields(fields, adata)
+            adata = merge_adata_obs_fields(fields, adata)
 
     check_fields([args.groupby, args.sample_key], adata)
 
@@ -274,7 +276,7 @@
         "-m",
         "--adata_obs_fields_to_merge",
         type=str,
-        help="Fields in adata.obs to merge, comma separated",
+        help="Fields in adata.obs to merge, comma separated. You can have more than one set of fields, separated by semi-colon ;",
     )
     parser.add_argument(
         "--groupby",