diff --git a/lib/galaxy/dataset_collections/__init__.py b/lib/galaxy/dataset_collections/__init__.py
index e50f3cab0f6..9419c5cc037 100644
--- a/lib/galaxy/dataset_collections/__init__.py
+++ b/lib/galaxy/dataset_collections/__init__.py
@@ -54,8 +54,12 @@ class DatasetCollectionsService(
     ):
         """
         """
-        if element_identifiers:
+        # Trust embedded, newly created objects created by tool subsystem.
+        trusted_identifiers = implicit_collection_info is not None
+
+        if element_identifiers and not trusted_identifiers:
             validate_input_element_identifiers( element_identifiers )
+
         dataset_collection = self.__create_dataset_collection(
             trans=trans,
             collection_type=collection_type,
diff --git a/lib/galaxy/dataset_collections/structure.py b/lib/galaxy/dataset_collections/structure.py
index 917ec1698ff..c21bdc9327a 100644
--- a/lib/galaxy/dataset_collections/structure.py
+++ b/lib/galaxy/dataset_collections/structure.py
@@ -78,7 +78,7 @@ class Tree( object ):
                 child_identifiers[ "name" ] = identifier
                 element_identifiers.append( child_identifiers )
             else:
-                element_identifiers.append( dict( name=identifier, src="hda", id=trans.security.encode_id( datasets[ 0 ].id ) ) )
+                element_identifiers.append( dict( name=identifier, __object__=datasets[ 0 ] ) )
 
             datasets = datasets[ len( child ): ]