diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index 990636db2c4..a4605653f18 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -171,6 +171,8 @@ def galactic_job_json(
             return replacement_record(value)
 
     def replacement_file(value):
+        if value.get('galaxy_id'):
+            return {"src": "hda", "id": value['galaxy_id']}
         file_path = value.get("location", None) or value.get("path", None)
         # format to match output definitions in tool, where did filetype come from?
         filetype = value.get("filetype", None) or value.get("format", None)
@@ -278,6 +280,8 @@ def galactic_job_json(
         return collection_element_identifiers
 
     def replacement_collection(value):
+        if value.get('galaxy_id'):
+            return {"src": "hdca", "id": value['galaxy_id']}
         assert "collection_type" in value
         collection_type = value["collection_type"]
         elements = to_elements(value, collection_type)
@@ -328,9 +332,10 @@ def _ensure_file_exists(file_path):
 
 class FileLiteralTarget:
 
-    def __init__(self, contents, **kwargs):
+    def __init__(self, contents, path=None, **kwargs):
         self.contents = contents
         self.properties = kwargs
+        self.path = path
 
     def __str__(self):
         return "FileLiteralTarget[path={}] with {}".format(self.path, self.properties)