diff --git a/lib/galaxy/util/xml_macros.py b/lib/galaxy/util/xml_macros.py
index 1bbbe530c19..4931523f32b 100644
--- a/lib/galaxy/util/xml_macros.py
+++ b/lib/galaxy/util/xml_macros.py
@@ -1,7 +1,7 @@
 import os
-from copy import copy, deepcopy
+from copy import deepcopy
 
-from galaxy.util import etree, parse_xml
+from galaxy.util import parse_xml
 
 REQUIRED_PARAMETER = object()
 
@@ -19,28 +19,25 @@ def load_with_references(path):
     if macros_el is None:
         return tree, []
 
-    # move the macros element to a separate tree
-    # otherwise included expand elements would be treated
-    # in the macro expansion
-    macros_tree = etree.ElementTree(copy(macros_el))
+    macros = {}
+    macro_paths = _import_macros(macros_el, path, macros)
     macros_el.clear()
-    org_macros_el = macros_el
-    macros_el = macros_tree.getroot()
-
-    macro_paths = _import_macros(macros_el, path)
 
     # Collect tokens
-    tokens = _macros_of_type(macros_el, 'token', lambda el: el.text or '')
+    tokens = {}
+    for m in macros.get('token', []):
+        tokens[m.get("name")] = m.text or ""
     tokens = expand_nested_tokens(tokens)
 
     # Expand xml macros
-    macro_dict = _macros_of_type(macros_el, 'xml', lambda el: XmlMacroDef(el))
+    macro_dict = {}
+    for m in macros.get('xml', []):
+        macro_dict[m.get("name")] = XmlMacroDef(m)
     _expand_macros([root], macro_dict, tokens)
 
     # reinsert template macro which are used during tool execution
-    for el in macros_el.xpath('//macro'):
-        if el.get('type') == 'template':
-            org_macros_el.append(el)
+    for m in macros.get("template", []):
+        macros_el.append(m)
     _expand_tokens_for_el(root, tokens)
     return tree, macro_paths
 
@@ -76,15 +73,15 @@ def imported_macro_paths(root):
     return _imported_macro_paths_from_el(macros_el)
 
 
-def _import_macros(macros_el, path):
+def _import_macros(macros_el, path, macros):
     """
     root the parsed XML tree
     path the path to the main xml document
     """
     xml_base_dir = os.path.dirname(path)
     if macros_el is not None:
-        macro_els, macro_paths = _load_macros(macros_el, xml_base_dir)
-        _xml_set_children(macros_el, macro_els)
+        macro_paths = _load_macros(macros_el, xml_base_dir, macros)
+        # _xml_set_children(macros_el, macro_els)
         return macro_paths
 
 
@@ -214,55 +211,48 @@ def _expand_yield_statements(macro_def, expand_el):
         _xml_replace(yield_el, expand_el_children)
 
 
-def _load_macros(macros_el, xml_base_dir):
-    macros = []
+def _load_macros(macros_el, xml_base_dir, macros):
     # Import macros from external files.
-    imported_macros, macro_paths = _load_imported_macros(macros_el, xml_base_dir)
-    macros.extend(imported_macros)
+    macro_paths = _load_imported_macros(macros_el, xml_base_dir, macros)
     # Load all directly defined macros.
-    macros.extend(_load_embedded_macros(macros_el, xml_base_dir))
-    return macros, macro_paths
+    _load_embedded_macros(macros_el, xml_base_dir, macros)
+    return macro_paths
 
 
-def _load_embedded_macros(macros_el, xml_base_dir):
-    macros = []
-
-    macro_els = []
+def _load_embedded_macros(macros_el, xml_base_dir, macros):
+    if macros_el is None:
+        return
     # attribute typed macro
-    if macros_el is not None:
-        macro_els = macros_el.findall("macro")
-    for macro in macro_els:
+    for macro in macros_el.iterfind("macro"):
         if 'type' not in macro.attrib:
             macro.attrib['type'] = 'xml'
-        macros.append(macro)
+        try:
+            macros[macro.attrib['type']].append(macro)
+        except KeyError:
+            macros[macro.attrib['type']] = [macro]
 
     # type shortcuts (<xml> is a shortcut for <macro type="xml",
     # likewise for <template>.
-    typed_tag = ['template', 'xml', 'token']
-    for tag in typed_tag:
-        macro_els = []
-        if macros_el is not None:
-            macro_els = macros_el.findall(tag)
-        for macro_el in macro_els:
+    for tag in ['template', 'xml', 'token']:
+        for macro_el in macros_el.iterfind(tag):
             macro_el.attrib['type'] = tag
             macro_el.tag = 'macro'
-            macros.append(macro_el)
-
-    return macros
+            try:
+                macros[tag].append(macro_el)
+            except KeyError:
+                macros[tag] = [macro_el]
 
 
-def _load_imported_macros(macros_el, xml_base_dir):
-    macros = []
+def _load_imported_macros(macros_el, xml_base_dir, macros):
     macro_paths = []
 
     for tool_relative_import_path in _imported_macro_paths_from_el(macros_el):
         import_path = \
             os.path.join(xml_base_dir, tool_relative_import_path)
         macro_paths.append(import_path)
-        file_macros, current_macro_paths = _load_macro_file(import_path, xml_base_dir)
-        macros.extend(file_macros)
+        current_macro_paths = _load_macro_file(import_path, xml_base_dir, macros)
         macro_paths.extend(current_macro_paths)
-    return macros, macro_paths
+    return macro_paths
 
 
 def _imported_macro_paths_from_el(macros_el):
@@ -276,10 +266,10 @@ def _imported_macro_paths_from_el(macros_el):
     return imported_macro_paths
 
 
-def _load_macro_file(path, xml_base_dir):
+def _load_macro_file(path, xml_base_dir, macros):
     tree = parse_xml(path, strip_whitespace=False)
     root = tree.getroot()
-    return _load_macros(root, xml_base_dir)
+    return _load_macros(root, xml_base_dir, macros)
 
 
 def _xml_set_children(element, new_children):