diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py
index 28f43bf7f61..b1e5d8e0c3e 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/upload.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py
@@ -14,6 +14,7 @@ from tool_shed.util import metadata_util
 from tool_shed.util import repository_dependency_util
 from tool_shed.util import tool_dependency_util
 from tool_shed.util import tool_util
+from tool_shed.util import xml_util
 
 from galaxy import eggs
 eggs.require( 'mercurial' )
@@ -131,7 +132,7 @@ class UploadController( BaseUIController ):
                         # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
                         altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
                         if altered:
-                            tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                            tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                             shutil.move( tmp_filename, full_path )
                         else:
                             shutil.move( uploaded_file_name, full_path )
@@ -140,7 +141,7 @@ class UploadController( BaseUIController ):
                         # are missing and if so, set them appropriately.
                         altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
                         if altered:
-                            tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                            tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                             shutil.move( tmp_filename, full_path )
                         else:
                             shutil.move( uploaded_file_name, full_path )
@@ -268,13 +269,13 @@ class UploadController( BaseUIController ):
                     # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
                     altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
                     if altered:
-                        tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                        tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                         shutil.move( tmp_filename, uploaded_file_name )
                 elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
                     # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
                     altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
                     if altered:
-                        tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                        tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                         shutil.move( tmp_filename, uploaded_file_name )
                 if ok:
                     repo_path = os.path.join( full_path, relative_path )
@@ -330,13 +331,13 @@ class UploadController( BaseUIController ):
                     # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
                     altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
                     if altered:
-                        tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                        tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                         shutil.move( tmp_filename, uploaded_file_name )
                 elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
                     # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
                     altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
                     if altered:
-                        tmp_filename = commit_util.create_and_write_tmp_file( root_elem )
+                        tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
                         shutil.move( tmp_filename, uploaded_file_name )
             return commit_util.handle_directory_changes( trans,
                                                          repository,
diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py
index 77a3bb4243d..0326d090c33 100644
--- a/lib/tool_shed/galaxy_install/install_manager.py
+++ b/lib/tool_shed/galaxy_install/install_manager.py
@@ -15,6 +15,7 @@ from tool_shed.util import datatype_util
 from tool_shed.util import metadata_util
 from tool_shed.util import tool_dependency_util
 from tool_shed.util import tool_util
+from tool_shed.util import xml_util
 from galaxy.util.odict import odict
 
 
@@ -37,13 +38,13 @@ class InstallManager( object ):
         self.proprietary_tool_confs = self.non_shed_tool_panel_configs
         self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number )
         # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
-        tree = util.parse_xml( migrated_tools_config )
+        tree = xml_util.parse_xml( migrated_tools_config )
         root = tree.getroot()
         self.tool_path = root.get( 'tool_path' )
         print "Repositories will be installed into configured tool_path location ", str( self.tool_path )
         # Parse tool_shed_install_config to check each of the tools.
         self.tool_shed_install_config = tool_shed_install_config
-        tree = util.parse_xml( tool_shed_install_config )
+        tree = xml_util.parse_xml( tool_shed_install_config )
         root = tree.getroot()
         self.tool_shed = suc.clean_tool_shed_url( root.get( 'name' ) )
         self.repository_owner = common_util.REPOSITORY_OWNER
@@ -107,7 +108,7 @@ class InstallManager( object ):
         tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
         # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
         migrated_tool_configs = []
-        tree = util.parse_xml( tools_xml_file_path )
+        tree = xml_util.parse_xml( tools_xml_file_path )
         root = tree.getroot()
         for elem in root:
             if elem.tag == 'repository':
@@ -116,7 +117,7 @@ class InstallManager( object ):
         # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
         tool_panel_elems = []
         for proprietary_tool_conf in self.proprietary_tool_confs:
-            tree = util.parse_xml( proprietary_tool_conf )
+            tree = xml_util.parse_xml( proprietary_tool_conf )
             root = tree.getroot()
             for elem in root:
                 if elem.tag == 'tool':
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
index 603e55eef38..f23bb1f19cb 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -10,6 +10,7 @@ import tool_shed.util.shed_util_common as suc
 import tool_shed.util.common_util as cu
 from tool_shed.util import encoding_util
 from tool_shed.util import tool_dependency_util
+from tool_shed.util import xml_util
 from galaxy.model.orm import and_
 from galaxy.web import url_for
 
@@ -478,7 +479,7 @@ def populate_actions_dict( app, dependent_install_dir, required_install_dir, too
     tool_dependency = None
     action_dict = {}
     if tool_dependencies_config:
-        required_td_tree = parse_xml( tool_dependencies_config )
+        required_td_tree = xml_util.parse_xml( tool_dependencies_config )
         if required_td_tree:
             required_td_root = required_td_tree.getroot()
             for required_td_elem in required_td_root:
@@ -623,17 +624,6 @@ def strip_path( fpath ):
         file_name = fpath
     return file_name
 
-def parse_xml( file_name ):
-    """Returns a parsed xml tree."""
-    try:
-        tree = ElementTree.parse( file_name )
-    except Exception, e:
-        print "Exception attempting to parse ", file_name, ": ", str( e )
-        return None
-    root = tree.getroot()
-    ElementInclude.include( root )
-    return tree
-
 def url_join( *args ):
     parts = []
     for arg in args:
diff --git a/lib/tool_shed/tool_shed_registry.py b/lib/tool_shed/tool_shed_registry.py
index 26a5aaa3d54..00b49ccc640 100644
--- a/lib/tool_shed/tool_shed_registry.py
+++ b/lib/tool_shed/tool_shed_registry.py
@@ -1,9 +1,8 @@
 import logging
 import sys
 import urllib2
-from galaxy.util import parse_xml
 from galaxy.util.odict import odict
-from xml.etree import ElementTree
+from tool_shed.util import xml_util
 
 log = logging.getLogger( __name__ )
 
@@ -15,7 +14,7 @@ class Registry( object ):
         self.tool_sheds_auth = odict()
         if root_dir and config:
             # Parse tool_sheds_conf.xml
-            tree = parse_xml( config )
+            tree = xml_util.parse_xml( config )
             root = tree.getroot()
             log.debug( 'Loading references to tool sheds from %s' % config )
             for elem in root.findall( 'tool_shed' ):
diff --git a/lib/tool_shed/util/commit_util.py b/lib/tool_shed/util/commit_util.py
index 55ee1b81fa9..8b041ede322 100644
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -9,7 +9,7 @@ from galaxy.util import json
 from galaxy.web import url_for
 import tool_shed.util.shed_util_common as suc
 from tool_shed.util import tool_util
-import xml.etree.ElementTree
+from tool_shed.util import xml_util
 from galaxy import eggs
 
 eggs.require( 'mercurial' )
@@ -60,17 +60,6 @@ def check_file_content_for_html_and_images( file_path ):
         message = 'The file "%s" contains image content.\n' % str( file_path )
     return message
 
-def create_and_write_tmp_file( root ):
-    tmp_str = '%s\n' % xml.etree.ElementTree.tostring( root, encoding='utf-8' )
-    fh = tempfile.NamedTemporaryFile( 'wb' )
-    tmp_filename = fh.name
-    fh.close()
-    fh = open( tmp_filename, 'wb' )
-    fh.write( '<?xml version="1.0"?>\n' )
-    fh.write( tmp_str )
-    fh.close()
-    return tmp_filename
-
 def get_upload_point( repository, **kwd ):
     upload_point = kwd.get( 'upload_point', None )
     if upload_point is not None:
@@ -198,7 +187,7 @@ def handle_repository_dependencies_definition( trans, repository_dependencies_co
     altered = False
     try:
         # Make sure we're looking at a valid repository_dependencies.xml file.
-        tree = suc.parse_xml( repository_dependencies_config )
+        tree = xml_util.parse_xml( repository_dependencies_config )
         root = tree.getroot()
     except Exception, e:
         error_message = "Error parsing %s in handle_repository_dependencies_definition: " % str( repository_dependencies_config )
@@ -245,7 +234,7 @@ def handle_tool_dependencies_definition( trans, tool_dependencies_config ):
     altered = False
     try:
         # Make sure we're looking at a valid tool_dependencies.xml file.
-        tree = suc.parse_xml( tool_dependencies_config )
+        tree = xml_util.parse_xml( tool_dependencies_config )
         root = tree.getroot()
     except Exception, e:
         error_message = "Error parsing %s in handle_tool_dependencies_definition: " % str( tool_dependencies_config )
diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py
index 6a004197a04..e237aab571f 100644
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -1,8 +1,8 @@
 import os
 import urllib2
-from galaxy import util
 from galaxy.util.odict import odict
 from tool_shed.util import encoding_util
+from tool_shed.util import xml_util
 
 REPOSITORY_OWNER = 'devteam'
 
@@ -11,7 +11,7 @@ def check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_scri
     tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
     # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config.
     migrated_tool_configs_dict = odict()
-    tree = util.parse_xml( tools_xml_file_path )
+    tree = xml_util.parse_xml( tools_xml_file_path )
     root = tree.getroot()
     tool_shed = root.get( 'name' )
     tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed )
@@ -48,7 +48,7 @@ def check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_scri
             # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
             missing_tool_configs_dict = odict()
             for tool_panel_config in tool_panel_configs:
-                tree = util.parse_xml( tool_panel_config )
+                tree = xml_util.parse_xml( tool_panel_config )
                 root = tree.getroot()
                 for elem in root:
                     if elem.tag == 'tool':
@@ -78,7 +78,7 @@ def get_non_shed_tool_panel_configs( app ):
     for config_filename in app.config.tool_configs:
         # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related.
         # <toolbox tool_path="../shed_tools">
-        tree = util.parse_xml( config_filename )
+        tree = xml_util.parse_xml( config_filename )
         root = tree.getroot()
         tool_path = root.get( 'tool_path', None )
         if tool_path is None:
diff --git a/lib/tool_shed/util/data_manager_util.py b/lib/tool_shed/util/data_manager_util.py
index 8f4ec2e6f21..c2b86946736 100644
--- a/lib/tool_shed/util/data_manager_util.py
+++ b/lib/tool_shed/util/data_manager_util.py
@@ -1,6 +1,6 @@
 import logging
 import os
-from galaxy import util
+from tool_shed.util import xml_util
 import tool_shed.util.shed_util_common as suc
 
 log = logging.getLogger( __name__ )
@@ -10,7 +10,7 @@ def data_manager_config_elems_to_xml_file( app, config_elems, config_filename ):
     fh = open( config_filename, 'wb' )
     fh.write( '<?xml version="1.0"?>\n<data_managers>\n' )#% ( shed_tool_conf_filename ))
     for elem in config_elems:
-        fh.write( util.xml_to_string( elem, pretty=True ) )
+        fh.write( xml_util.xml_to_string( elem ) )
     fh.write( '</data_managers>\n' )
     fh.close()
 
@@ -21,7 +21,7 @@ def install_data_managers( app, shed_data_manager_conf_filename, metadata_dict,
         for tool_tup in repository_tools_tups:
             repository_tools_by_guid[ tool_tup[ 1 ] ] = dict( tool_config_filename=tool_tup[ 0 ], tool=tool_tup[ 2 ] )
         # Load existing data managers.
-        config_elems = [ elem for elem in util.parse_xml( shed_data_manager_conf_filename ).getroot() ]
+        config_elems = [ elem for elem in xml_util.parse_xml( shed_data_manager_conf_filename ).getroot() ]
         repo_data_manager_conf_filename = metadata_dict['data_manager'].get( 'config_filename', None )
         if repo_data_manager_conf_filename is None:
             log.debug( "No data_manager_conf.xml file has been defined." )
@@ -29,13 +29,13 @@ def install_data_managers( app, shed_data_manager_conf_filename, metadata_dict,
         data_manager_config_has_changes = False
         relative_repo_data_manager_dir = os.path.join( shed_config_dict.get( 'tool_path', '' ), relative_install_dir )
         repo_data_manager_conf_filename = os.path.join( relative_repo_data_manager_dir, repo_data_manager_conf_filename )
-        tree = util.parse_xml( repo_data_manager_conf_filename )
+        tree = xml_util.parse_xml( repo_data_manager_conf_filename )
         root = tree.getroot()
         for elem in root:
             if elem.tag == 'data_manager':
                 data_manager_id = elem.get( 'id', None )
                 if data_manager_id is None:
-                    log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( util.xml_to_string( elem ) ) )
+                    log.error( "A data manager was defined that does not have an id and will not be installed:\n%s" % ( xml_util.xml_to_string( elem ) ) )
                     continue
                 data_manager_dict = metadata_dict['data_manager'].get( 'data_managers', {} ).get( data_manager_id, None )
                 if data_manager_dict is None:
@@ -77,7 +77,7 @@ def install_data_managers( app, shed_data_manager_conf_filename, metadata_dict,
                 if data_manager:
                     rval.append( data_manager )
             else:
-                log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, util.xml_to_string( elem ) ) )
+                log.warning( "Encountered unexpected element '%s':\n%s" % ( elem.tag, xml_util.xml_to_string( elem ) ) )
             config_elems.append( elem )
             data_manager_config_has_changes = True
         # Persist the altered shed_data_manager_config file.
@@ -89,7 +89,7 @@ def remove_from_data_manager( app, repository ):
     metadata_dict = repository.metadata
     if metadata_dict and 'data_manager' in metadata_dict:
         shed_data_manager_conf_filename = app.config.shed_data_manager_config_file
-        tree = util.parse_xml( shed_data_manager_conf_filename )
+        tree = xml_util.parse_xml( shed_data_manager_conf_filename )
         root = tree.getroot()
         assert root.tag == 'data_managers', 'The file provided (%s) for removing data managers from is not a valid data manager xml file.' % ( shed_data_manager_conf_filename )
         guids = [ data_manager_dict.get( 'guid' ) for data_manager_dict in metadata_dict.get( 'data_manager', {} ).get( 'data_managers', {} ).itervalues() if 'guid' in data_manager_dict ]
diff --git a/lib/tool_shed/util/datatype_util.py b/lib/tool_shed/util/datatype_util.py
index 98267bdef95..78f84ad0b18 100644
--- a/lib/tool_shed/util/datatype_util.py
+++ b/lib/tool_shed/util/datatype_util.py
@@ -2,7 +2,7 @@ import logging
 import os
 import tempfile
 from galaxy import eggs
-from galaxy import util
+from tool_shed.util import xml_util
 import tool_shed.util.shed_util_common as suc
 
 import pkg_resources
@@ -24,7 +24,7 @@ def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_
     has been initialized, the registry's contents cannot be overridden by conflicting data types.
     """
     try:
-        tree = util.parse_xml( datatypes_config )
+        tree = xml_util.parse_xml( datatypes_config )
     except Exception, e:
         log.debug( "Error parsing %s, exception: %s" % ( datatypes_config, str( e ) ) )
         return None, None
@@ -83,9 +83,9 @@ def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_
     fd, proprietary_datatypes_config = tempfile.mkstemp()
     os.write( fd, '<?xml version="1.0"?>\n' )
     os.write( fd, '<datatypes>\n' )
-    os.write( fd, '%s' % util.xml_to_string( registration ) )
+    os.write( fd, '%s' % xml_util.xml_to_string( registration ) )
     if sniffers:
-        os.write( fd, '%s' % util.xml_to_string( sniffers ) )
+        os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) )
     os.write( fd, '</datatypes>\n' )
     os.close( fd )
     os.chmod( proprietary_datatypes_config, 0644 )
diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py
index 1c4cf86febf..269f9798296 100644
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -17,6 +17,7 @@ from tool_shed.util import common_install_util
 from tool_shed.util import readme_util
 from tool_shed.util import tool_dependency_util
 from tool_shed.util import tool_util
+from tool_shed.util import xml_util
 
 import pkg_resources
 
@@ -363,7 +364,7 @@ def generate_data_manager_metadata( app, repository, repo_dir, data_manager_conf
                               'error_messages': [] }
     metadata_dict[ 'data_manager' ] = data_manager_metadata
     try:
-        tree = util.parse_xml( data_manager_config_filename )
+        tree = xml_util.parse_xml( data_manager_config_filename )
     except Exception, e:
         # We are not able to load any data managers.
         error_message = 'There was an error parsing your Data Manager config file "%s": %s' % ( data_manager_config_filename, e )
@@ -638,7 +639,7 @@ def generate_metadata_for_changeset_revision( app, repository, changeset_revisio
                                  or checkers.check_bz2( full_path )[ 0 ] or checkers.check_zip( full_path ) ):
                             try:
                                 # Make sure we're looking at a tool config and not a display application config or something else.
-                                element_tree = util.parse_xml( full_path )
+                                element_tree = xml_util.parse_xml( full_path )
                                 element_tree_root = element_tree.getroot()
                                 is_tool = element_tree_root.tag == 'tool'
                             except Exception, e:
@@ -751,7 +752,7 @@ def generate_repository_dependency_metadata( app, repository_dependencies_config
     error_message = ''
     try:
         # Make sure we're looking at a valid repository_dependencies.xml file.
-        tree = util.parse_xml( repository_dependencies_config )
+        tree = xml_util.parse_xml( repository_dependencies_config )
         root = tree.getroot()
         xml_is_valid = root.tag == 'repositories'
     except Exception, e:
diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py
index 99dad0252d6..5570517a792 100644
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -14,7 +14,7 @@ from galaxy.datatypes import checkers
 from galaxy.model.orm import and_
 import sqlalchemy.orm.exc
 from tool_shed.util import common_util
-from xml.etree import ElementTree as XmlET
+from tool_shed.util import xml_util
 from galaxy import eggs
 import pkg_resources
 
@@ -37,17 +37,6 @@ MAX_CONTENT_SIZE = 1048576
 MAX_DISPLAY_SIZE = 32768
 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" )
 
-
-class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ):
-    def __init__ ( self, html=0, target=None ):
-        XmlET.XMLTreeBuilder.__init__( self, html, target )
-        self._parser.CommentHandler = self.handle_comment
-    
-    def handle_comment ( self, data ):
-        self._target.start( XmlET.Comment, {} )
-        self._target.data( data )
-        self._target.end( XmlET.Comment )
-
 new_repo_email_alert_template = """
 Sharable link:         ${sharable_link}
 Repository name:       ${repository_name}
@@ -188,7 +177,7 @@ def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ):
     os.write( fd, '<?xml version="1.0"?>\n' )
     os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) )
     for elem in config_elems:
-        os.write( fd, '%s' % util.xml_to_string( elem, pretty=True ) )
+        os.write( fd, '%s' % xml_util.xml_to_string( elem ) )
     os.write( fd, '</toolbox>\n' )
     os.close( fd )
     shutil.move( filename, os.path.abspath( config_filename ) )
@@ -346,7 +335,7 @@ def generate_tool_panel_dict_from_shed_tool_conf_entries( app, repository ):
         file_name = strip_path( tool_config )
         guids_and_configs[ guid ] = file_name
     # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. 
-    tree = util.parse_xml( shed_tool_conf )
+    tree = xml_util.parse_xml( shed_tool_conf )
     root = tree.getroot()
     for elem in root:
         if elem.tag == 'tool':
@@ -1084,13 +1073,6 @@ def parse_repository_dependency_tuple( repository_dependency_tuple, contains_err
         prior_installation_required = util.asbool( str( prior_installation_required ) )
         return tool_shed, name, owner, changeset_revision, prior_installation_required
 
-def parse_xml( fname ):
-    """Returns a parsed xml tree with comments in tact."""
-    fobj = open( fname, 'r' )
-    tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() )
-    fobj.close()
-    return tree
-
 def pretty_print( dict=None ):
     if dict:
         return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' )
@@ -1271,7 +1253,7 @@ def update_in_shed_tool_config( app, repository ):
     for tool_config_filename, guid, tool in repository_tools_tups:
         guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None )
     config_elems = []
-    tree = util.parse_xml( shed_tool_conf )
+    tree = xml_util.parse_xml( shed_tool_conf )
     root = tree.getroot()
     for elem in root:
         if elem.tag == 'section':
diff --git a/lib/tool_shed/util/tool_util.py b/lib/tool_shed/util/tool_util.py
index aebdaf11ff9..b398e05e356 100644
--- a/lib/tool_shed/util/tool_util.py
+++ b/lib/tool_shed/util/tool_util.py
@@ -12,6 +12,7 @@ from galaxy.tools import parameters
 from galaxy.tools.parameters import dynamic_options
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.web.form_builder import SelectField
+from tool_shed.util import xml_util
 import tool_shed.util.shed_util_common as suc
 
 import pkg_resources
@@ -36,7 +37,7 @@ def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ):
     shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
     tool_path = shed_tool_conf_dict[ 'tool_path' ]
     config_elems = []
-    tree = util.parse_xml( shed_tool_conf )
+    tree = xml_util.parse_xml( shed_tool_conf )
     root = tree.getroot()
     for elem in root:
         config_elems.append( elem )
@@ -803,7 +804,7 @@ def load_tool_from_tmp_config( trans, repo, repository_id, ctx, ctx_file, work_d
     message = ''
     tmp_tool_config = suc.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir )
     if tmp_tool_config:
-        element_tree = util.parse_xml( tmp_tool_config )
+        element_tree = xml_util.parse_xml( tmp_tool_config )
         element_tree_root = element_tree.getroot()
         # Look for code files required by the tool config.
         tmp_code_files = []
@@ -845,7 +846,7 @@ def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ):
     shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
     tool_path = shed_tool_conf_dict[ 'tool_path' ]
     config_elems = []
-    tree = util.parse_xml( shed_tool_conf )
+    tree = xml_util.parse_xml( shed_tool_conf )
     root = tree.getroot()
     for elem in root:
         config_elems.append( elem )
diff --git a/lib/tool_shed/util/xml_util.py b/lib/tool_shed/util/xml_util.py
new file mode 100644
index 00000000000..67b9fabea96
--- /dev/null
+++ b/lib/tool_shed/util/xml_util.py
@@ -0,0 +1,43 @@
+import logging
+import os
+import tempfile
+from xml.etree import ElementTree as XmlET
+import xml.etree.ElementTree
+
+log = logging.getLogger( __name__ )
+
+
+class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ):
+    def __init__ ( self, html=0, target=None ):
+        XmlET.XMLTreeBuilder.__init__( self, html, target )
+        self._parser.CommentHandler = self.handle_comment
+    
+    def handle_comment ( self, data ):
+        self._target.start( XmlET.Comment, {} )
+        self._target.data( data )
+        self._target.end( XmlET.Comment )
+
+def create_and_write_tmp_file( elem ):
+    tmp_str = xml_to_string( elem )
+    fh = tempfile.NamedTemporaryFile( 'wb' )
+    tmp_filename = fh.name
+    fh.close()
+    fh = open( tmp_filename, 'wb' )
+    fh.write( '<?xml version="1.0"?>\n' )
+    fh.write( tmp_str )
+    fh.close()
+    return tmp_filename
+
+def parse_xml( file_name ):
+    """Returns a parsed xml tree with comments intact."""
+    try:
+        fobj = open( file_name, 'r' )
+        tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() )
+        fobj.close()
+    except Exception, e:
+        log.exception( "Exception attempting to parse %s: %s" % ( str( file_name ), str( e ) ) )
+        return None
+    return tree
+
+def xml_to_string( elem, encoding='utf-8' ):
+    return '%s\n' % xml.etree.ElementTree.tostring( elem, encoding=encoding )