Preserve tags (ignoring collection handling for now) when running tools.

galaxyproject · Mar 2, 2017 · 9f4764f · 9f4764f
1 parent d3840c5
commit 9f4764f
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
@@ -214,6 +214,7 @@ def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=Tru
         # format.
         input_ext = 'data' if tool.profile < 16.04 else "input"
         input_dbkey = incoming.get( "dbkey", "?" )
+        preserved_tags = []
         for name, data in reversed(inp_data.items()):
             if not data:
                 data = NoneDataset( datatypes_registry=app.datatypes_registry )
@@ -234,6 +235,9 @@ def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=Tru
             if identifier is not None:
                 incoming[ "%s|__identifier__" % name ] = identifier
 
+            for tag in data.tags:
+                preserved_tags.append(tag)
+
         # Collect chromInfo dataset and add as parameters to incoming
         ( chrom_info, db_dataset ) = app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id != 'CONVERTER_fasta_to_len' )
         if db_dataset:
@@ -303,6 +307,9 @@ def handle_output( name, output, hidden=None ):
                 trans.sa_session.add( data )
                 trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions, new=True )
 
+            for tag in preserved_tags:
+                data.tags.append(tag.copy())
+
             # Must flush before setting object store id currently.
             # TODO: optimize this.
             trans.sa_session.flush()