diff --git a/lib/galaxy/tools/stock.py b/lib/galaxy/tools/stock.py
index 1a86354f1370..eead325e644a 100644
--- a/lib/galaxy/tools/stock.py
+++ b/lib/galaxy/tools/stock.py
@@ -7,6 +7,7 @@
 # Set GALAXY_INCLUDES_ROOT from tool shed to point this at a Galaxy root
 # (once we are running the tool shed from packages not rooted with Galaxy).
 import galaxy.tools
+from galaxy.tool_util.loader_directory import looks_like_a_tool_xml
 from galaxy.tool_util.parser import get_tool_source
 from galaxy.util import galaxy_directory
 from galaxy.util.resources import files
@@ -26,7 +27,7 @@ def stock_tool_sources():
 
 
 def _walk_directory_for_tools(path):
-    if path.is_file() and path.name.endswith(".xml"):
+    if path.is_file() and not path.name.endswith("tool_conf.xml") and looks_like_a_tool_xml(path):
         yield path
     elif path.is_dir():
         for directory in path.iterdir():