diff --git a/lib/galaxy/tools/data_fetch.py b/lib/galaxy/tools/data_fetch.py
index 21d5365194fb..0f117b55ad5c 100644
--- a/lib/galaxy/tools/data_fetch.py
+++ b/lib/galaxy/tools/data_fetch.py
@@ -375,8 +375,8 @@ def walk_extra_files(items, prefix=""):
                 assert path
                 datatype.groom_dataset_content(path)
 
-            if datatype.file_ext == "directory":
-                CompressedFile.extract(path, extra_files_path)
+            if ext == "directory" and not deferred and path:
+                CompressedFile(path).extract(extra_files_path)
                 staged_extra_files = extra_files_path
 
             if len(transform) > 0: