diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py
index dad6deaafaf..03b601b2eca 100644
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -197,7 +197,7 @@ class TwillTestCase( unittest.TestCase ):
         filename = os.path.join( *path )
         file(filename, 'wt').write(buffer.getvalue())
 
-    def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', space_to_tab=False, metadata=None, composite_data=None, shed_tool_id=None ):
+    def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', space_to_tab=False, metadata=None, composite_data=None, name=None, shed_tool_id=None, wait=True ):
         """
         Uploads a file.  If shed_tool_id has a value, we're testing tools migrated from the distribution to the tool shed,
         so the tool-data directory of test data files is contained in the installed tool shed repository.
@@ -218,12 +218,19 @@ class TwillTestCase( unittest.TestCase ):
                 filename = self.get_filename( filename, shed_tool_id=shed_tool_id )
                 tc.formfile( "tool_form", "file_data", filename )
                 tc.fv( "tool_form", "space_to_tab", space_to_tab )
+                if name:
+                    # NAME is a hidden form element, so the following prop must
+                    # set to use it.
+                    tc.config("readonly_controls_writeable", 1)
+                    tc.fv( "tool_form", "NAME", name )
             tc.submit( "runtool_btn" )
             self.home()
         except AssertionError, err:
             errmsg = "Uploading file resulted in the following exception.  Make sure the file (%s) exists.  " % filename
             errmsg += str( err )
             raise AssertionError( errmsg )
+        if not wait:
+            return
         # Make sure every history item has a valid hid
         hids = self.get_hids_in_history()
         for hid in hids:
diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py
index 009dc686152..f6e1be0e4fd 100644
--- a/test/functional/test_toolbox.py
+++ b/test/functional/test_toolbox.py
@@ -25,8 +25,11 @@ class ToolTestCase( TwillTestCase ):
         test_history = galaxy_interactor.new_history()
 
         # Upload any needed files
+        upload_waits = []
         for test_data in testdef.test_data():
-            galaxy_interactor.stage_data( test_data, shed_tool_id )
+            upload_waits.append( galaxy_interactor.stage_data_async( test_data, shed_tool_id ) )
+        for upload_wait in upload_waits:
+            upload_wait()
 
         data_list = galaxy_interactor.run_tool( testdef )
         self.assertTrue( data_list )
@@ -70,20 +73,24 @@ class GalaxyInteractorTwill( object ):
     def __init__( self, twill_test_case ):
         self.twill_test_case = twill_test_case
 
-    def stage_data( self, test_data, shed_tool_id ):
+    def stage_data_async( self, test_data, shed_tool_id, async=True ):
+            name = test_data.get( 'name', None )
+            if name:
+                async = False
             self.twill_test_case.upload_file( test_data['fname'],
                                               ftype=test_data['ftype'],
                                               dbkey=test_data['dbkey'],
                                               metadata=test_data['metadata'],
                                               composite_data=test_data['composite_data'],
-                                              shed_tool_id=shed_tool_id )
-            name = test_data.get('name', None)
+                                              shed_tool_id=shed_tool_id,
+                                              wait=(not async) )
             if name:
                 hda_id = self.twill_test_case.get_history_as_data_list()[-1].get( 'id' )
                 try:
                     self.twill_test_case.edit_hda_attribute_info( hda_id=str(hda_id), new_name=name )
                 except:
                     print "### call to edit_hda failed for hda_id %s, new_name=%s" % (hda_id, name)
+            return lambda: self.twill_test_case.wait()
 
     def run_tool( self, testdef ):
         # We need to handle the case where we've uploaded a valid compressed file since the upload