Run "#main resolved object by default

Author: Anton Khodak

cwltool/load_tool.py

@@ -281,15 +281,21 @@ def make_tool(document_loader,  # type: Loader
     """Make a Python CWL object."""
     resolveduri = document_loader.resolve_ref(uri)[0]
 
+    processobj = None
     if isinstance(resolveduri, list):
         if len(resolveduri) == 1:
             processobj = resolveduri[0]
         else:
-            raise WorkflowException(
-                u"Tool file contains graph of multiple objects, must specify "
-                "one of #%s" % ", #".join(
-                    urllib.parse.urldefrag(i["id"])[1] for i in resolveduri
-                    if "id" in i))
+            for obj in resolveduri:
+                if obj['id'].endswith('#main'):
+                    processobj = obj
+                    break
+            if not processobj:
+                raise WorkflowException(
+                    u"Tool file contains graph of multiple objects, must specify "
+                    "one of #%s" % ", #".join(
+                        urllib.parse.urldefrag(i["id"])[1] for i in resolveduri
+                        if "id" in i))
     elif isinstance(resolveduri, dict):
         processobj = resolveduri
     else: