diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index e22d96737464..3051ba669171 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -599,7 +599,12 @@ def dir_listing(dir_path):
                             if extra_file_class == "File":
                                 ec = get_dataset(output_metadata, filename=path)
                                 ec["basename"] = ec_basename
-                                ec_properties = output_properties(pseudo_location=pseudo_location, **ec)
+                                download_url = (
+                                    output_metadata["download_url"] + f"?filename={urllib.parse.quote_plus(path)}"
+                                )
+                                ec_properties = output_properties(
+                                    pseudo_location=pseudo_location, download_url=download_url, **ec
+                                )
                             elif extra_file_class == "Directory":
                                 ec_properties = {}
                                 ec_properties["class"] = "Directory"
diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index ca8c54b7fc80..8c7f87919055 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -267,6 +267,10 @@ def conformance_tests_gen(directory, filename="conformance_tests.yaml"):
 
 def output_to_disk(output, download_folder):
     if isinstance(output, dict):
+        if "secondaryFiles" in output:
+            output["secondaryFiles"] = [
+                output_to_disk(secondary, download_folder=download_folder) for secondary in output["secondaryFiles"]
+            ]
         if "basename" in output:
             download_path = os.path.join(download_folder, output["basename"])
             download_to_file(output["location"], download_path)