diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py
index 39f02b477f2..e7860f62d60 100644
--- a/lib/galaxy/web/base/controllers/admin.py
+++ b/lib/galaxy/web/base/controllers/admin.py
@@ -7,6 +7,7 @@ from galaxy.util import inflector
 from galaxy.web.form_builder import CheckboxField
 from string import punctuation as PUNCTUATION
 import galaxy.queue_worker
+from markupsafe import escape
 
 from tool_shed.util import shed_util_common as suc
 
@@ -28,7 +29,7 @@ class Admin( object ):
     @web.expose
     @web.require_admin
     def index( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', ''  ) )
         status = kwd.get( 'status', 'done' )
         if trans.webapp.name == 'galaxy':
             installed_repositories = trans.install_model.context.query( trans.install_model.ToolShedRepository ).first()
@@ -46,7 +47,7 @@ class Admin( object ):
     @web.expose
     @web.require_admin
     def center( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', ''  ) )
         status = kwd.get( 'status', 'done' )
         if trans.webapp.name == 'galaxy':
             return trans.fill_template( '/webapps/galaxy/admin/center.mako',
diff --git a/lib/galaxy/webapps/demo_sequencer/controllers/common.py b/lib/galaxy/webapps/demo_sequencer/controllers/common.py
index a467a03206a..10ec385bfd4 100644
--- a/lib/galaxy/webapps/demo_sequencer/controllers/common.py
+++ b/lib/galaxy/webapps/demo_sequencer/controllers/common.py
@@ -4,6 +4,7 @@ from galaxy import util
 import time, socket, urllib, urllib2, base64, copy
 from galaxy.util.json import *
 from urllib import quote_plus, unquote_plus
+from markupsafe import escape
 
 import logging
 log = logging.getLogger( __name__ )
@@ -16,7 +17,7 @@ class CommonController( BaseUIController ):
         titles = util.listify( titles )
         JobId = util.restore_text( kwd.get( 'JobId', '' ) )
         sample_id = util.restore_text( kwd.get( 'sample_id', '' ) )
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         status = kwd.get( 'status', 'done' )
         redirect_delay = trans.app.sequencer_actions_registry.redirect_delay
         sequencer_redirects = copy.deepcopy( trans.app.sequencer_actions_registry.sequencer_redirects )
@@ -144,7 +145,7 @@ class CommonController( BaseUIController ):
         titles = util.restore_text( kwd.get( 'titles', '' ) )
         JobId = util.restore_text( kwd.get( 'JobId', '' ) )
         sample_id = util.restore_text( kwd.get( 'sample_id', '' ) )
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         status = kwd.get( 'status', 'done' )
         url, http_method, request_params, response_type = request_tup
         url = unquote_plus( url )
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py
index f5743ba594d..15221c3392d 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -17,6 +17,7 @@ from galaxy.web.framework.helpers import grids, time_ago
 from galaxy.web.params import QuotaParamParser
 from tool_shed.util import common_util
 from tool_shed.util import encoding_util
+from markupsafe import escape
 
 log = logging.getLogger( __name__ )
 
@@ -838,7 +839,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
     @web.expose
     @web.require_admin
     def review_tool_migration_stages( self, trans, **kwd ):
-        message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
         status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
         migration_stages_dict = odict()
         migration_modules = []
@@ -870,13 +871,13 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaP
     @web.expose
     @web.require_admin
     def view_datatypes_registry( self, trans, **kwd ):
-        message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
         status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
         return trans.fill_template( 'admin/view_datatypes_registry.mako', message=message, status=status )
 
     @web.expose
     @web.require_admin
     def view_tool_data_tables( self, trans, **kwd ):
-        message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
         status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
         return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status )
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index d424915a698..db45f5266ca 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -8,6 +8,7 @@ from galaxy import util
 from galaxy.web.form_builder import CheckboxField
 from galaxy.util import json
 from galaxy.model.orm import or_
+from markupsafe import escape
 
 import tool_shed.repository_types.util as rt_util
 
@@ -72,7 +73,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def browse_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
         return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
@@ -169,7 +170,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def browse_tool_dependency( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
         tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] )
@@ -197,7 +198,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def browse_tool_sheds( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
                                     message=message,
@@ -230,7 +231,7 @@ class AdminToolshed( AdminGalaxy ):
         require the same entry.  For now we'll never delete entries from config.shed_tool_data_table_config,
         but we may choose to do so in the future if it becomes necessary.
         """
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         remove_from_disk = kwd.get( 'remove_from_disk', '' )
         remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk )
@@ -442,7 +443,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.require_admin
     def import_workflow( self, trans, workflow_name, repository_id, **kwd ):
         """Import a workflow contained in an installed tool shed repository into Galaxy."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if workflow_name:
             workflow_name = encoding_util.tool_shed_decode( workflow_name )
@@ -479,7 +480,7 @@ class AdminToolshed( AdminGalaxy ):
         tool shed repository.
         """
         # Get the tool_shed_repository from one of the tool_dependencies.
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         err_msg = ''
         tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
@@ -512,7 +513,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.require_admin
     def install_latest_repository_revision( self, trans, **kwd ):
         """Install the latest installable revision of a repository that has been previously installed."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if repository_id is not None:
@@ -589,7 +590,7 @@ class AdminToolshed( AdminGalaxy ):
         updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
         updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
         encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
         if 'install_tool_dependencies_with_update_button' in kwd:
@@ -665,7 +666,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def manage_repositories( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
         if 'operation' in kwd:
@@ -744,7 +745,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def manage_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if repository_id is None:
@@ -808,7 +809,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def manage_repository_tool_dependencies( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
         if tool_dependency_ids:
@@ -890,7 +891,7 @@ class AdminToolshed( AdminGalaxy ):
     def manage_tool_dependencies( self, trans, **kwd ):
         # This method is called when tool dependencies are being installed.  See the related manage_repository_tool_dependencies
         # method for managing the tool dependencies for a specified installed tool shed repository.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
         repository_id = kwd.get( 'repository_id', None )
@@ -978,7 +979,7 @@ class AdminToolshed( AdminGalaxy ):
             message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
             message += 'Shed wiki for all of the details.'
             return trans.show_error_message( message )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         shed_tool_conf = kwd.get( 'shed_tool_conf', None )
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
@@ -1314,7 +1315,7 @@ class AdminToolshed( AdminGalaxy ):
         and tool dependencies of the repository.
         """
         rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app )
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd[ 'id' ]
         tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id )
@@ -1450,7 +1451,7 @@ class AdminToolshed( AdminGalaxy ):
         Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as
         each repository's tool dependencies.
         """
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if not repository_id:
@@ -1715,7 +1716,7 @@ class AdminToolshed( AdminGalaxy ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd )
         else:
-            message = kwd.get( 'message', ''  )
+            message = escape( kwd.get( 'message', '' ) )
             status = kwd.get( 'status', 'done' )
         repositories_select_field = irmm.build_repository_ids_select_field()
         return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
@@ -1852,7 +1853,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def uninstall_tool_dependencies( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
         if not tool_dependency_ids:
@@ -1897,7 +1898,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.require_admin
     def update_to_changeset_revision( self, trans, **kwd ):
         """Update a cloned repository to the latest revision possible."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         tool_shed_url = kwd.get( 'tool_shed_url', '' )
         # Handle protocol changes over time.
@@ -2070,7 +2071,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def update_tool_shed_status_for_installed_repository( self, trans, all_installed_repositories=False, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if all_installed_repositories:
             success_count = 0
@@ -2112,7 +2113,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.expose
     @web.require_admin
     def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id )
         repository_metadata = repository.metadata
@@ -2146,7 +2147,7 @@ class AdminToolshed( AdminGalaxy ):
     @web.require_admin
     def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ):
         """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if workflow_name:
             workflow_name = encoding_util.tool_shed_decode( workflow_name )
diff --git a/lib/galaxy/webapps/galaxy/controllers/library_admin.py b/lib/galaxy/webapps/galaxy/controllers/library_admin.py
index e7ff588159a..bba28f5401f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library_admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_admin.py
@@ -5,8 +5,9 @@ import galaxy.util
 
 from galaxy import web
 from galaxy.web.base.controller import BaseUIController
-from galaxy.web.framework.helpers import escape, grids, time_ago
+from galaxy.web.framework.helpers import grids, time_ago
 from library_common import get_comptypes, lucene_search, whoosh_search
+from markupsafe import escape
 # from galaxy.model.orm import *
 
 log = logging.getLogger( __name__ )
@@ -148,7 +149,7 @@ class LibraryAdmin( BaseUIController ):
     @web.expose
     @web.require_admin
     def create_library( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', ''  ) )
         status = kwd.get( 'status', 'done' )
         if kwd.get( 'create_library_button', False ):
             name = kwd.get( 'name', 'No name' )
diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py
index f74627b0a4e..d7264e45ddc 100644
--- a/lib/galaxy/webapps/galaxy/controllers/library_common.py
+++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -20,7 +20,7 @@ from galaxy.util.json import dumps, loads
 from galaxy.util.streamball import StreamBall
 from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems
 from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field
-from galaxy.web.framework.helpers import escape
+from markupsafe import escape
 from galaxy.model.orm import and_, eagerload_all
 
 # Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled.
@@ -93,7 +93,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
 
     @web.expose
     def browse_library( self, trans, cntrller='library', **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         # If use_panels is True, the library is being accessed via an external link
         # which did not originate from within the Galaxy instance, and the library will
@@ -121,7 +121,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
             hidden_folder_ids = util.listify( kwd.get( 'hidden_folder_ids', '' ) )
             if created_ldda_ids and not message:
                 message = "%d datasets are uploading in the background to the library '%s' (each is selected).  "  % \
-                    ( len( created_ldda_ids.split( ',' ) ), library.name )
+                    ( len( created_ldda_ids.split( ',' ) ), escape( library.name ) )
                 message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the "
                 message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset."
                 status = "info"
@@ -152,7 +152,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                                 message=escape( message ),
                                                 status=escape( status ) )
             except Exception, e:
-                message = 'Error attempting to display contents of library (%s): %s.' % ( str( library.name ), str( e ) )
+                message = 'Error attempting to display contents of library (%s): %s.' % ( escape( str( library.name ) ), str( e ) )
                 status = 'error'
         default_action = kwd.get( 'default_action', None )
 
@@ -164,7 +164,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                                           status=status ) )
     @web.expose
     def library_info( self, trans, cntrller, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
@@ -223,7 +223,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def library_permissions( self, trans, cntrller, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
@@ -269,7 +269,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -345,7 +345,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def folder_info( self, trans, cntrller, id, library_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -401,7 +401,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def folder_permissions( self, trans, cntrller, id, library_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -450,7 +450,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -505,7 +505,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
             old_name = ldda.name
             new_name = kwd.get( 'name', '' )
             new_info = kwd.get( 'info', '' )
-            new_message = kwd.get( 'message', '' )
+            new_message = escape( kwd.get( 'message', ''  ) )
             if not new_name:
                 message = 'Enter a valid name'
                 status = 'error'
@@ -602,7 +602,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         show_associated_hdas_and_lddas = util.string_as_bool( kwd.get( 'show_associated_hdas_and_lddas', False ) )
@@ -650,7 +650,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -787,9 +787,9 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
-        ldda_message = kwd.get( 'ldda_message', '' )
+        ldda_message = escape( kwd.get( 'ldda_message', '' ) )
         deleted = util.string_as_bool( kwd.get( 'deleted', False ) )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1046,7 +1046,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                 dataset_upload_inputs.append( input )
         # Library-specific params
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         server_dir = kwd.get( 'server_dir', '' )
         if replace_dataset not in [ None, 'None' ]:
@@ -1256,9 +1256,9 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
 
     @web.expose
     def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
-        ldda_message = kwd.get( 'ldda_message', '' )
+        ldda_message = escape( kwd.get( 'ldda_message', '' ) )
         show_deleted = kwd.get( 'show_deleted', False )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
         replace_id = kwd.get( 'replace_id', None )
@@ -1547,7 +1547,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                                           status='error' ) )
     @web.expose
     def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1595,7 +1595,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1642,7 +1642,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                                     status=escape( status ) )
     @web.expose
     def make_library_item_public( self, trans, cntrller, library_id, item_type, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1703,7 +1703,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
                     rval += '%s %i %s%s %s\r\n' % ( crc, size, self.url_base, quoted_fname, relpath )
                 return rval
         # Perform an action on a list of library datasets.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -1979,7 +1979,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
         # - a select list option for acting on multiple selected datasets within a library
         #   ( ldda_ids is a comma separated string of ldda ids )
         # - a menu option for a library dataset search result set ( ldda_ids is a comma separated string of ldda ids )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -2102,7 +2102,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
     def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ):
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         is_admin = ( trans.user_is_admin() and cntrller == 'library_admin' )
         current_user_roles = trans.get_current_user_roles()
@@ -2152,7 +2152,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
         #   'ldda' and item_id is a comma separated string of ldda ids )
         # - a menu option for a library dataset search result set ( item_type is 'ldda' and item_id is a
         #   comma separated string of ldda ids )
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
@@ -2723,7 +2723,7 @@ def sort_by_attr( seq, attr ):
     return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
 def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
     """Return display of results from a full-text lucene search of data libraries."""
-    message = kwd.get( 'message', ''  )
+    message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     full_url = "%s/find?%s" % ( search_url, urllib.urlencode( { "kwd" : search_term } ) )
     response = urllib2.urlopen( full_url )
@@ -2733,7 +2733,7 @@ def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
     return status, message, get_sorted_accessible_library_items( trans, cntrller, lddas, 'name' )
 def whoosh_search( trans, cntrller, search_term, **kwd ):
     """Return display of results from a full-text whoosh search of data libraries."""
-    message = kwd.get( 'message', ''  )
+    message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     ok = True
     if whoosh_search_enabled:
diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py
index 8bb3b5ca1f9..8ae9d1e20fc 100644
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -28,9 +28,10 @@ from galaxy.web.base.controller import CreatesUsersMixin
 from galaxy.web.base.controller import CreatesApiKeysMixin
 from galaxy.web.form_builder import CheckboxField
 from galaxy.web.form_builder import build_select_field
-from galaxy.web.framework.helpers import time_ago, grids, escape
+from galaxy.web.framework.helpers import time_ago, grids
 from datetime import datetime, timedelta
 from galaxy.util import hash_util, biostar
+from markupsafe import escape
 
 log = logging.getLogger( __name__ )
 
@@ -254,7 +255,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
         if not trans.app.config.enable_openid:
             return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' )
         use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) )
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', ''  ) )
         status = kwd.get( 'status', 'done' )
         email = kwd.get( 'email', '' )
         username = kwd.get( 'username', '' )
@@ -502,7 +503,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
         """
         Function validates numerous cases that might happen during the login time.
         """
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'error' )
         email = kwd.get( 'email', '' )
         password = kwd.get( 'password', '' )
@@ -719,7 +720,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
         email = util.restore_text( kwd.get( 'email', '' ) )
         password = kwd.get( 'password', '' )
         username = util.restore_text( kwd.get( 'username', '' ) )
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', ''  ) )
         status = kwd.get( 'status', 'done' )
         is_admin = cntrller == 'admin' and trans.user_is_admin()
         user = self.create_user( trans=trans, email=email, username=username, password=password )
@@ -1093,7 +1094,7 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat
     def reset_password( self, trans, email=None, **kwd ):
         if trans.app.config.smtp_server is None:
             return trans.show_error_message( "Mail is not configured for this Galaxy instance.  Please contact your local Galaxy administrator." )
-        message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) ))
+        message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) )
         status = kwd.get( 'status', 'done' )
         if kwd.get( 'reset_password_button', False ):
             reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first()
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 219338b4160..dae6c3c4231 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -22,7 +22,7 @@ from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import error, url_for
 from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
 from galaxy.web.framework.formbuilder import form
-from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape
+from galaxy.web.framework.helpers import grids, time_ago, to_unicode
 from galaxy.workflow.modules import WorkflowModuleInjector
 from galaxy.workflow.modules import MissingToolException
 from galaxy.workflow.modules import module_factory, is_tool_module_type
@@ -37,6 +37,7 @@ from galaxy.workflow.steps import (
     order_workflow_steps_with_levels,
 )
 from galaxy.workflow.render import WorkflowCanvas, MARGIN, LINE_SPACING
+from markupsafe import escape
 
 
 class StoredWorkflowListGrid( grids.Grid ):
@@ -1021,7 +1022,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         """
         url = kwd.get( 'url', '' )
         workflow_text = kwd.get( 'workflow_text', '' )
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         import_button = kwd.get( 'import_button', False )
         # The special Galaxy integration landing page's URL on myExperiment
diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py
index 543dc891fc1..5fbacd14619 100644
--- a/lib/galaxy/webapps/reports/controllers/users.py
+++ b/lib/galaxy/webapps/reports/controllers/users.py
@@ -9,17 +9,19 @@ import pkg_resources
 pkg_resources.require( "SQLAlchemy >= 0.4" )
 import sqlalchemy as sa
 import logging
+from markupsafe import escape
+
 log = logging.getLogger( __name__ )
 
 class Users( BaseUIController ):
     @web.expose
     def registered_users( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         num_users = trans.sa_session.query( galaxy.model.User ).count()
         return trans.fill_template( '/webapps/reports/registered_users.mako', num_users=num_users, message=message )
     @web.expose
     def registered_users_per_month( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.User.table.c.create_time ) ).label( 'date' ),
                          sa.func.count( galaxy.model.User.table.c.id ).label( 'num_users' ) ),
                        from_obj = [ galaxy.model.User.table ],
@@ -36,7 +38,7 @@ class Users( BaseUIController ):
                                     message=message )
     @web.expose
     def specified_month( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
         specified_month = specified_date[ :7 ]
@@ -66,7 +68,7 @@ class Users( BaseUIController ):
                                     message=message )
     @web.expose
     def specified_date( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         # If specified_date is not received, we'll default to the current month
         specified_date = kwd.get( 'specified_date', datetime.utcnow().strftime( "%Y-%m-%d" ) )
         year, month, day = map( int, specified_date.split( "-" ) )
@@ -95,7 +97,7 @@ class Users( BaseUIController ):
                                     message=message )
     @web.expose
     def last_access_date( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         not_logged_in_for_days = kwd.get( 'not_logged_in_for_days', 90 )
         if not not_logged_in_for_days:
             not_logged_in_for_days = 0
@@ -120,7 +122,7 @@ class Users( BaseUIController ):
 
     @web.expose
     def user_disk_usage( self, trans, **kwd ):
-        message = util.restore_text( kwd.get( 'message', '' ) )
+        message = escape( util.restore_text( kwd.get( 'message', '' ) ) )
         user_cutoff = int( kwd.get( 'user_cutoff', 60 ) )
         # disk_usage isn't indexed
         users = sorted( trans.sa_session.query( galaxy.model.User ).all(), key=operator.attrgetter( 'disk_usage' ), reverse=True )
diff --git a/lib/galaxy/webapps/tool_shed/controllers/admin.py b/lib/galaxy/webapps/tool_shed/controllers/admin.py
index 118be31bcfb..73a314788fc 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/admin.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py
@@ -3,6 +3,7 @@ import logging
 from galaxy import util
 from galaxy.util import inflector
 from galaxy import web
+from markupsafe import escape
 
 from galaxy.web.base.controller import BaseUIController
 from galaxy.web.base.controllers.admin import Admin
@@ -121,7 +122,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def create_category( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         name = kwd.get( 'name', '' ).strip()
         description = kwd.get( 'description', '' ).strip()
@@ -154,7 +155,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def delete_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
@@ -197,7 +198,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def delete_repository_metadata( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
@@ -221,7 +222,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def edit_category( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if not id:
@@ -306,7 +307,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def regenerate_statistics( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if 'regenerate_statistics_button' in kwd:
             trans.app.shed_counter.generate_statistics()
@@ -352,7 +353,7 @@ class AdminController( BaseUIController, Admin ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
         else:
-            message = util.restore_text( kwd.get( 'message', ''  ) )
+            message = escape( util.restore_text( kwd.get( 'message', ''  ) ) )
             status = kwd.get( 'status', 'done' )
         repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids',
                                                                            multiple=True,
@@ -366,7 +367,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def undelete_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
@@ -417,7 +418,7 @@ class AdminController( BaseUIController, Admin ):
         # TODO: We should probably eliminate the Category.deleted column since it really makes no
         # sense to mark a category as deleted (category names and descriptions can be changed instead).
         # If we do this, and the following 2 methods can be eliminated.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
@@ -445,7 +446,7 @@ class AdminController( BaseUIController, Admin ):
         # This method should only be called for a Category that has previously been deleted.
         # Purging a deleted Category deletes all of the following from the database:
         # - RepoitoryCategoryAssociations where category_id == Category.id
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
@@ -473,7 +474,7 @@ class AdminController( BaseUIController, Admin ):
     @web.expose
     @web.require_admin
     def undelete_category( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if id:
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index c1b99dbd306..9d130f653be 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -6,6 +6,7 @@ from time import gmtime
 from time import strftime
 from datetime import date
 from datetime import datetime
+from markupsafe import escape
 
 from galaxy import util
 from galaxy import web
@@ -385,7 +386,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
                                                                   action='reviewed_repositories_i_own' ) )
             elif operation == "repositories_by_category":
                 category_id = kwd.get( 'id', None )
-                message = kwd.get( 'message', '' )
+                message = escape( kwd.get( 'message', '' ) )
                 status = kwd.get( 'status', 'done' )
                 return trans.response.send_redirect( web.url_for( controller='repository',
                                                                   action='browse_repositories_in_category',
@@ -721,9 +722,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def browse_repository( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
-        commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
+        commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
         # Update repository files for browsing.
@@ -891,7 +892,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     def check_for_updates( self, trans, **kwd ):
         """Handle a request from a local Galaxy instance."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         # If the request originated with the UpdateRepositoryManager, it will not include a galaxy_url.
         galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
@@ -976,7 +977,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def contact_owner( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app,
@@ -995,7 +996,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def create_galaxy_docker_image( self, trans, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_ids = util.listify( kwd.get( 'id', '' ) )
         if 'operation' in kwd:
@@ -1051,7 +1052,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def create_repository( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         categories = suc.get_categories( trans )
         if not categories:
@@ -1108,7 +1109,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset
         # revisions that may be associated with the repository.  Revisions are not marked as not downlaodable
         # because those that have installed the repository must be allowed to get updates.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -1164,7 +1165,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
         tv = tool_validator.ToolValidator( trans.app )
@@ -1229,7 +1230,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def export( self, trans, repository_id, changeset_revision, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         export_repository_dependencies = kwd.get( 'export_repository_dependencies', '' )
         repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -1309,7 +1310,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def find_tools( self, trans, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
         if 'operation' in kwd:
@@ -1400,7 +1401,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def find_workflows( self, trans, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
         if 'operation' in kwd:
@@ -2020,13 +2021,13 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def help( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd )
 
     @web.expose
     def import_capsule( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         capsule_file_name = kwd.get( 'capsule_file_name', None )
         encoded_file_path = kwd.get( 'encoded_file_path', None )
@@ -2069,7 +2070,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def index( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         # See if there are any RepositoryMetadata records since menu items require them.
         repository_metadata = trans.sa_session.query( trans.model.RepositoryMetadata ).first()
@@ -2151,7 +2152,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'error' )
         render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
         tv = tool_validator.ToolValidator( trans.app )
@@ -2203,7 +2204,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "manage email alerts" )
     def manage_email_alerts( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         new_repo_alert = kwd.get( 'new_repo_alert', '' )
         new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert )
@@ -2234,7 +2235,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "manage repository" )
     def manage_repository( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repository_type = kwd.get( 'repository_type', str( repository.type ) )
@@ -2500,7 +2501,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "manage repository administrators" )
     def manage_repository_admins( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
@@ -2558,7 +2559,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "multi select email alerts" )
     def multi_select_email_alerts( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if 'operation' in kwd:
             operation = kwd[ 'operation' ].lower()
@@ -2607,7 +2608,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -2714,7 +2715,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "rate repositories" )
     def rate_repository( self, trans, **kwd ):
         """ Rate a repository and return updated rating data. """
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if not id:
@@ -2787,7 +2788,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
         else:
-            message = kwd.get( 'message', ''  )
+            message = escape( kwd.get( 'message', '' ) )
             status = kwd.get( 'status', 'done' )
         repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids',
                                                                            multiple=True,
@@ -2800,9 +2801,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def select_files_to_delete( self, trans, id, **kwd ):
-        message = kwd.get( 'message', '' )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
-        commit_message = kwd.get( 'commit_message', 'Deleted selected files' )
+        commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repo_dir = repository.repo_path( trans.app )
         repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
@@ -3145,7 +3146,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def upload_capsule( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         url = kwd.get( 'url', '' )
         if 'upload_capsule_button' in kwd:
@@ -3175,7 +3176,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def view_changelog( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3210,7 +3211,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def view_changeset( self, trans, id, ctx_str, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3302,7 +3303,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def view_repository( self, trans, id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
@@ -3390,7 +3391,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
 
     @web.expose
     def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
         repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
@@ -3471,7 +3472,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ):
         """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image."""
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
         if workflow_name:
diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
index 023c72f6f7f..69e11819e9c 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py
@@ -2,6 +2,7 @@ import logging
 import os
 
 from sqlalchemy.sql.expression import func
+from markupsafe import escape
 
 from galaxy import util
 from galaxy import web
@@ -40,7 +41,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "approve repository review" )
     def approve_repository_review( self, trans, **kwd ):
         # The value of the received id is the encoded review id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         encoded_review_id = kwd[ 'id' ]
         review = review_util.get_review( trans.app, encoded_review_id )
@@ -74,7 +75,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "browse review" )
     def browse_review( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         review = review_util.get_review( trans.app, kwd[ 'id' ] )
         repository = review.repository
@@ -105,7 +106,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "create component" )
     def create_component( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         name = kwd.get( 'name', '' )
         description = kwd.get( 'description', '' )
@@ -136,7 +137,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "create review" )
     def create_review( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
@@ -201,7 +202,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "edit component" )
     def edit_component( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         id = kwd.get( 'id', None )
         if not id:
@@ -232,7 +233,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "edit review" )
     def edit_review( self, trans, **kwd ):
         # The value of the received id is the encoded review id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         review_id = kwd.get( 'id', None )
         review = review_util.get_review( trans.app, review_id )
@@ -408,7 +409,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "manage repositories reviewed by me" )
     def manage_repositories_reviewed_by_me( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         if 'operation' in kwd:
             kwd[ 'mine' ] = True
@@ -475,7 +476,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "manage repository reviews" )
     def manage_repository_reviews( self, trans, mine=False, **kwd ):
         # The value of the received id is the encoded repository id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if repository_id:
@@ -524,7 +525,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "manage repository reviews of revision" )
     def manage_repository_reviews_of_revision( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
@@ -547,7 +548,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "repository reviews by user" )
     def repository_reviews_by_user( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
 
         if 'operation' in kwd:
@@ -573,7 +574,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.expose
     @web.require_login( "reviewed repositories i own" )
     def reviewed_repositories_i_own( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         # The value of the received id is the encoded repository id.
         if 'operation' in kwd:
@@ -592,7 +593,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
     @web.require_login( "select previous review" )
     def select_previous_review( self, trans, **kwd ):
         # The value of the received id is the encoded repository id.
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
         repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
         changeset_revision = kwd.get( 'changeset_revision', None )
diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py
index 62dbcb93581..17a4f871d1a 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/upload.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py
@@ -9,6 +9,7 @@ from galaxy import util
 from galaxy import web
 from galaxy.datatypes import checkers
 from galaxy.web.base.controller import BaseUIController
+from markupsafe import escape
 
 from tool_shed.dependencies import attribute_handlers
 from tool_shed.galaxy_install import dependency_display
@@ -34,9 +35,9 @@ class UploadController( BaseUIController ):
     @web.expose
     @web.require_login( 'upload', use_panels=True )
     def upload( self, trans, **kwd ):
-        message = kwd.get( 'message', ''  )
+        message = escape( kwd.get( 'message', '' ) )
         status = kwd.get( 'status', 'done' )
-        commit_message = kwd.get( 'commit_message', 'Uploaded'  )
+        commit_message = escape( kwd.get( 'commit_message', 'Uploaded'  ) )
         category_ids = util.listify( kwd.get( 'category_id', '' ) )
         categories = suc.get_categories( trans.app )
         repository_id = kwd.get( 'repository_id', '' )
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 1a4c3ee0da0..8af826321a0 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -7,6 +7,7 @@ from galaxy import util
 from galaxy import web
 from galaxy.web.form_builder import build_select_field
 from galaxy.webapps.tool_shed.model import directory_hash_id
+from markupsafe import escape
 
 from tool_shed.dependencies.repository import relation_builder
 
@@ -256,7 +257,7 @@ def get_role_by_id( app, role_id ):
 
 def handle_role_associations( app, role, repository, **kwd ):
     sa_session = app.model.context.current
-    message = kwd.get( 'message', '' )
+    message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     repository_owner = repository.user
     if kwd.get( 'manage_role_associations_button', False ):