diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 347f107f172..e36a0523fb4 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -69,7 +69,7 @@ from galaxy.model.item_attrs import Dictifiable
 from galaxy.model import Workflow
 from tool_shed.util import common_util
 from tool_shed.util import shed_util_common as suc
-from .loader import load_tool, template_macro_params
+from .loader import load_tool, template_macro_params, raw_tool_xml_tree
 from .execute import execute as execute_job
 from .wrappers import (
     ToolParameterValueWrapper,
@@ -2989,6 +2989,21 @@ class Tool( object, Dictifiable ):
     def get_default_history_by_trans( self, trans, create=False ):
         return trans.get_history( create=create )
 
+    @classmethod
+    def get_externally_referenced_paths( self, path ):
+        """ Return relative paths to externally referenced files by the tool
+        described by file at `path`. External components should not assume things
+        about the structure of tool xml files (this is the tool's responsibility).
+        """
+        tree = raw_tool_xml_tree(path)
+        root = tree.getroot()
+        external_paths = []
+        for code_elem in root.findall( 'code' ):
+            external_path = code_elem.get( 'file' )
+            if external_path:
+                external_paths.append( external_path )
+        return external_paths
+
 
 class OutputParameterJSONTool( Tool ):
     """
diff --git a/lib/galaxy/tools/loader.py b/lib/galaxy/tools/loader.py
index d696ce680e1..85082647997 100644
--- a/lib/galaxy/tools/loader.py
+++ b/lib/galaxy/tools/loader.py
@@ -10,7 +10,7 @@ def load_tool(path):
     """
     Loads tool from file system and preprocesses tool macros.
     """
-    tree = parse_xml(path)
+    tree = raw_tool_xml_tree(path)
     root = tree.getroot()
 
     _import_macros(root, path)
@@ -38,6 +38,14 @@ def template_macro_params(root):
     return param_dict
 
 
+def raw_tool_xml_tree(path):
+    """ Load raw (no macro expansion) tree representation of tool represented
+    at the specified path.
+    """
+    tree = parse_xml(path)
+    return tree
+
+
 def _import_macros(root, path):
     tool_dir = os.path.dirname(path)
     macros_el = root.find('macros')
diff --git a/lib/tool_shed/tools/tool_validator.py b/lib/tool_shed/tools/tool_validator.py
index 09afe10c971..dc3910c1695 100644
--- a/lib/tool_shed/tools/tool_validator.py
+++ b/lib/tool_shed/tools/tool_validator.py
@@ -3,6 +3,7 @@ import logging
 import os
 import tempfile
 
+from galaxy.tools import Tool
 from galaxy.tools import parameters
 from galaxy.tools.parameters import dynamic_options
 
@@ -311,15 +312,14 @@ class ToolValidator( object ):
         message = ''
         tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir )
         if tmp_tool_config:
-            element_tree, error_message = xml_util.parse_xml( tmp_tool_config )
-            if element_tree is None:
+            tool_element, error_message = xml_util.parse_xml( tmp_tool_config )
+            if tool_element is None:
                 return tool, message
-            element_tree_root = element_tree.getroot()
-            # Look for code files required by the tool config.
+            # Look for external files required by the tool config.
             tmp_code_files = []
-            for code_elem in element_tree_root.findall( 'code' ):
-                code_file_name = code_elem.get( 'file' )
-                tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir )
+            external_paths = Tool.get_externally_referenced_paths( tmp_tool_config )
+            for path in external_paths:
+                tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, path, work_dir )
                 if tmp_code_file_name:
                     tmp_code_files.append( tmp_code_file_name )
             tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config )
diff --git a/test/unit/tools/test_tool_external_files.py b/test/unit/tools/test_tool_external_files.py
new file mode 100644
index 00000000000..369bd8d22a6
--- /dev/null
+++ b/test/unit/tools/test_tool_external_files.py
@@ -0,0 +1,26 @@
+""" Unit test logic related to finding externally referenced files in tool
+descriptions.
+"""
+import tempfile
+import os
+import shutil
+from galaxy.tools import Tool
+
+
+def test_finds_external_code_file():
+    assert __external_files("""<tool><code file="foo.py" /></tool>""") == ["foo.py"]
+
+
+def test_finds_skips_empty_code_file_attribute():
+    assert __external_files("""<tool><code /></tool>""") == []
+
+
+def __external_files(contents):
+    base_path = tempfile.mkdtemp()
+    try:
+        tool_path = os.path.join(base_path, "tool.xml")
+        with open(tool_path, "w") as f:
+            f.write(contents)
+        return Tool.get_externally_referenced_paths(tool_path)
+    finally:
+        shutil.rmtree(base_path)