Rewrite CWL tools.

galaxyproject · Nov 20, 2019 · 9a8855d · 9a8855d
1 parent bfbdae9
commit 9a8855d
Showing 1 changed file with 9 additions and 1 deletion.
diff --git a/lib/galaxy/tool_util/cwl/schema.py b/lib/galaxy/tool_util/cwl/schema.py
@@ -14,6 +14,7 @@
 
 RawProcessReference = namedtuple("RawProcessReference", ["loading_context", "process_object", "uri"])
 ResolvedProcessDefinition = namedtuple("ResolvedProcessDefinition", ["loading_context", "uri", "raw_process_reference"])
+REWRITE_EXPRESSIONS = True
 
 
 class SchemaLoader(object):
@@ -37,8 +38,15 @@ def loading_context(self):
         return loading_context
 
     def raw_process_reference(self, path, loading_context=None):
-        uri = "file://" + os.path.abspath(path)
+        path = os.path.abspath(path)
+        uri = "file://" + path
         loading_context = loading_context or self.loading_context()
+        if REWRITE_EXPRESSIONS and not uri.endswith(".galaxy"):
+            galaxy_path = os.path.abspath(path) + ".galaxy"
+            from cwl_utils import etools_to_clt
+            etools_to_clt.main([path, galaxy_path])
+            galaxy_uri = "file://" + galaxy_path
+            uri = galaxy_uri
         loading_context, process_object, uri = load_tool.fetch_document(uri, loadingContext=loading_context)
         return RawProcessReference(loading_context, process_object, uri)