Merge pull request #2494 from jmchilton/galaxy-lib-update-2

Update against latest galaxy-lib.

lib/galaxy/tools/cwl/parser.py

@@ -237,8 +237,8 @@ class JobProxy(object):
         if self._cwl_job is None:
             self._cwl_job = self._tool_proxy._tool.job(
                 self._input_dict,
-                self._job_directory,
                 self._output_callback,
+                basedir=self._job_directory,
                 use_container=False
             ).next()
             self._is_command_line_job = hasattr(self._cwl_job, "command_line")

lib/galaxy/tools/cwl/schema.py

@@ -61,7 +61,6 @@ class SchemaLoader(object):
         tool = load_tool.make_tool(
             process_definition.document_loader,
             process_definition.avsc_names,
-            process_definition.process_object,
             process_definition.metadata,
             process_definition.raw_process_reference.uri,
             make_tool,

lib/galaxy/tools/parser/cwl.py

@@ -60,6 +60,12 @@ class CwlToolSource(ToolSource):
 
         return environment_variables
 
+    def parse_edam_operations(self):
+        return []
+
+    def parse_edam_topics(self):
+        return []
+
     def parse_help(self):
         return self.tool_proxy.description() or ""