diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index e605d4c72d4..58b407b5d27 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -594,7 +594,7 @@ class InputModule(WorkflowModule):
         progress.set_outputs_for_input(invocation_step, step_outputs)
 
     def recover_mapping(self, invocation_step, progress):
-        progress.set_outputs_for_input(invocation_step)
+        progress.set_outputs_for_input(invocation_step, already_persisted=True)
 
 
 class InputDataModule(InputModule):
@@ -1305,17 +1305,6 @@ class ToolModule(WorkflowModule):
 
         return complete
 
-    def recover_mapping(self, invocation_step, progress):
-        outputs = {}
-
-        for output_dataset_assoc in invocation_step.output_datasets:
-            outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
-
-        for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
-            outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
-
-        progress.set_step_outputs(invocation_step, outputs)
-
     def _effective_post_job_actions(self, step):
         effective_post_job_actions = step.post_job_actions[:]
         for key, value in self.runtime_post_job_actions.items():
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 3336139eab3..ae20dcb943f 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -405,7 +405,7 @@ class WorkflowProgress(object):
         else:
             return step_outputs[output_name]
 
-    def set_outputs_for_input(self, invocation_step, outputs=None):
+    def set_outputs_for_input(self, invocation_step, outputs=None, already_persisted=False):
         step = invocation_step.workflow_step
 
         if outputs is None:
@@ -420,7 +420,7 @@ class WorkflowProgress(object):
             elif step_id in self.inputs_by_step_id:
                 outputs['output'] = self.inputs_by_step_id[step_id]
 
-        self.set_step_outputs(invocation_step, outputs)
+        self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
 
     def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
         step = invocation_step.workflow_step