diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 74047973f2a..34a8bb5d294 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2159,11 +2159,17 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                                                    all_repository_dependencies=None,
                                                                                                    handled_key_rd_dicts=None )
                 if str( repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION:
-                    # Handle messaging for orphan tool dependencies.
-                    orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata )
-                    if orphan_message:
-                        message += orphan_message
+                    # Handle messaging for resetting repository type to the optimal value.
+                    change_repository_type_message = tool_dependency_util.generate_message_for_repository_type_change( trans, repository )
+                    if change_repository_type_message:
+                        message += change_repository_type_message
                         status = 'warning'
+                    else:
+                        # Handle messaging for orphan tool dependency definitions.
+                        orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata )
+                        if orphan_message:
+                            message += orphan_message
+                            status = 'warning'
         if is_malicious:
             if trans.app.security_agent.can_push( trans.app, trans.user, repository ):
                 message += malicious_error_can_push
diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py
index 51919e19f4c..1dd31c340e3 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/upload.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py
@@ -207,15 +207,20 @@ class UploadController( BaseUIController ):
                     else:
                         metadata_dict = {}
                     if str( repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION:
-                        # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
-                        # or some other problem.  Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository),
-                        # so warning messages are important because orphans are always valid.  The repository owner must be warned in case they did not intend to define an
-                        # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition.
-                        # Handle messaging for orphan tool dependencies.
-                        orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict )
-                        if orphan_message:
-                            message += orphan_message
+                        change_repository_type_message = tool_dependency_util.generate_message_for_repository_type_change( trans, repository )
+                        if change_repository_type_message:
+                            message += change_repository_type_message
                             status = 'warning'
+                        else:
+                            # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
+                            # or some other problem.  Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository),
+                            # so warning messages are important because orphans are always valid.  The repository owner must be warned in case they did not intend to define an
+                            # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition.
+                            # Handle messaging for orphan tool dependencies.
+                            orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict )
+                            if orphan_message:
+                                message += orphan_message
+                                status = 'warning'
                     # Handle messaging for invalid tool dependencies.
                     invalid_tool_dependencies_message = tool_dependency_util.generate_message_for_invalid_tool_dependencies( metadata_dict )
                     if invalid_tool_dependencies_message:
diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index 315584ce861..a9287e133c7 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -906,13 +906,13 @@ def generate_tool_dependency_metadata( app, repository, changeset_revision, repo
                                                                  repository_dependency_tups=invalid_repository_dependency_tups,
                                                                  is_valid=False,
                                                                  description=description )
-    # We need to continue to restrict the behavior of orphan tool dependencies, possibly eliminating them altoghether at some point.
+    # We need to continue to restrict the behavior for defining orphan tool dependencies, possibly eliminating them altoghether at some point.
     check_for_orphan_tool_dependencies = False
     if app.name == 'tool_shed':
-        if repository.type == rt_util.UNRESTRICTED and 'tools' not in metadata_dict:
-            check_for_orphan_tool_dependencies = True
-        elif 'tools' in metadata_dict:
+        if repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and not repository.can_change_type_to( app, rt_util.TOOL_DEPENDENCY_DEFINITION ):
             check_for_orphan_tool_dependencies = True
+    elif 'tools' in metadata_dict:
+        check_for_orphan_tool_dependencies = True
     if check_for_orphan_tool_dependencies:
         # Determine and store orphan tool dependencies.
         orphan_tool_dependencies = get_orphan_tool_dependencies( metadata_dict )
diff --git a/lib/tool_shed/util/tool_dependency_util.py b/lib/tool_shed/util/tool_dependency_util.py
index 77d560d6a39..2d2f7854799 100644
--- a/lib/tool_shed/util/tool_dependency_util.py
+++ b/lib/tool_shed/util/tool_dependency_util.py
@@ -150,14 +150,17 @@ def generate_message_for_orphan_tool_dependencies( trans, repository, metadata_d
                         version = requirements_dict[ 'version' ]
                         message += "<b>* name:</b> %s, <b>type:</b> %s, <b>version:</b> %s<br/>" % ( str( name ), str( type ), str( version ) )
                     message += "<br/>"
-            elif repository.can_change_type_to( trans.app, rt_util.TOOL_DEPENDENCY_DEFINITION ):
-                tool_dependency_definition_type_class = trans.app.repository_types_registry.get_class_by_label( rt_util.TOOL_DEPENDENCY_DEFINITION )
-                message += "This repository currently contains a single file named <b>%s</b>.  If additional files will " % suc.TOOL_DEPENDENCY_DEFINITION_FILENAME
-                message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % tool_dependency_definition_type_class.label
-            else:
-                message += "This repository contains no tools, so it's defined tool dependencies are considered orphans within this repository.<br/>"
     return message
 
+def generate_message_for_repository_type_change( trans, repository ):
+    message = ''
+    if repository.can_change_type_to( trans.app, rt_util.TOOL_DEPENDENCY_DEFINITION ):
+        tool_dependency_definition_type_class = trans.app.repository_types_registry.get_class_by_label( rt_util.TOOL_DEPENDENCY_DEFINITION )
+        message += "This repository currently contains a single file named <b>%s</b>.  If additional files will " % suc.TOOL_DEPENDENCY_DEFINITION_FILENAME
+        message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % tool_dependency_definition_type_class.label
+    return message
+                
+                
 def get_download_url_for_platform( url_templates, platform_info_dict ):
     '''
     Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return
diff --git a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
index e5c862e0cbb..bf69b157710 100644
--- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
+++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
@@ -54,7 +54,7 @@ class TestComplexRepositoryDependencies( ShedTwillTestCase ):
                           strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], 
                           strings_not_displayed=[] )
         # Visit the manage repository page for package_bwa_0_5_9_0100.
-        self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] )
+        self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'will not be', 'to this repository' ] )
 
     def test_0010_create_bwa_base_repository( self ):
         '''Create and populate bwa_base_0100.'''