diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index 71e993a3efa6..4c57663cb090 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -625,7 +625,11 @@ def dir_listing(dir_path):
                     "basename": basename,
                     "listing": listing,
                 }
-                _handle_pseudo_location(properties, pseudo_location=pseudo_location, download_url=output_metadata["download_url"] + "?to_ext=directory")
+                _handle_pseudo_location(
+                    properties,
+                    pseudo_location=pseudo_location,
+                    download_url=output_metadata["download_url"] + "?to_ext=directory",
+                )
 
                 extra_files = get_extra_files(output_metadata)
                 for extra_file in extra_files:
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index 764f51fd124d..b4acb65be5ff 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -266,6 +266,14 @@ def conformance_tests_gen(directory, filename="conformance_tests.yaml"):
             yield conformance_test
 
 
+def to_local_location(listing, location):
+    for item in listing:
+        if "basename" in item:
+            item["location"] = f"file://{os.path.join(location[len('file://'):], item['basename'])}"
+            if "listing" in item:
+                to_local_location(item["listing"], location=item["location"])
+
+
 def output_to_disk(output, download_folder):
     if isinstance(output, dict):
         if "secondaryFiles" in output:
@@ -274,9 +282,17 @@ def output_to_disk(output, download_folder):
             ]
         if "basename" in output:
             download_path = os.path.join(download_folder, output["basename"])
-            download_to_file(output["location"], download_path)
+            if output["class"] == "Directory":
+                zip_path = f"{download_path}.zip"
+                download_to_file(output["location"], zip_path)
+                CompressedFile(zip_path).extract(download_folder)
+                os.remove(zip_path)
+            else:
+                download_to_file(output["location"], download_path)
             output["path"] = download_path
             output["location"] = f"file://{download_path}"
+            if "listing" in output:
+                to_local_location(output["listing"], output["location"])
             return output
         else:
             new_output = {}