Delay tool exec for discovered & mapped-over input

We should only finalize collections up until the map over depth,
as indicated by the TODO that is now obsolete.
Fixes https://github.com/galaxyproject/galaxy/issues/5867 and probably
a bunch of other issues where workflows don't run to completion.

lib/galaxy/model/__init__.py

@@ -3445,14 +3445,13 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
         self.populated_state = DatasetCollection.populated_states.FAILED
         self.populated_state_message = message
 
-    def finalize(self):
+    def finalize(self, collection_type_description):
         # All jobs have written out their elements - everything should be populated
         # but might not be - check that second case! (TODO)
         self.mark_as_populated()
-        if self.has_subcollections:
-            # THIS IS WRONG - SHOULD ONLY BE TO THE DEPTH OF THE MAP OVER.
+        if self.has_subcollections and collection_type_description.has_subcollections():
             for element in self.elements:
-                element.child_collection.finalize()
+                element.child_collection.finalize(collection_type_description.child_collection_type_description())
 
     @property
     def dataset_instances(self):

lib/galaxy/tools/execute.py

@@ -314,7 +314,9 @@ class ExecutionTracker(object):
                     implicit_collection_jobs = implicit_collection.implicit_collection_jobs
                     implicit_collection_jobs.populated_state = "ok"
                     trans.sa_session.add(implicit_collection_jobs)
-                implicit_collection.collection.finalize()
+                implicit_collection.collection.finalize(
+                    collection_type_description=self.collection_info.structure.collection_type_description
+                )
                 trans.sa_session.add(implicit_collection.collection)
         trans.sa_session.flush()