Fix for auto-detect metadata tool running second set metadata call.

lib/galaxy/jobs/__init__.py

@@ -1495,6 +1495,12 @@ class JobWrapper( object ):
         just copy these files directly to the ulimate destination.
         """
         return output_path
+    
+    @property
+    def requires_setting_metadata( self ):
+        if self.tool:
+            return self.tool.requires_setting_metadata
+        return False
 
 
 class TaskWrapper(JobWrapper):

lib/galaxy/jobs/runners/__init__.py

@@ -176,7 +176,7 @@ class BaseJobRunner( object ):
 
         # Append metadata setting commands, we don't want to overwrite metadata
         # that was copied over in init_meta(), as per established behavior
-        if include_metadata:
+        if include_metadata and job_wrapper.requires_setting_metadata:
             commands += "; cd %s; " % os.path.abspath( os.getcwd() )
             commands += job_wrapper.setup_external_metadata(
                             exec_dir = os.path.abspath( os.getcwd() ),

lib/galaxy/tools/__init__.py

@@ -971,6 +971,7 @@ class Tool( object, Dictifiable ):
     """
 
     tool_type = 'default'
+    requires_setting_metadata = True
     default_tool_action = DefaultToolAction
     dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' )
 
@@ -3134,6 +3135,8 @@ class SetMetadataTool( Tool ):
     dataset.
     """
     tool_type = 'set_metadata'
+    requires_setting_metadata = False
+    
     def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ):
         for name, dataset in inp_data.iteritems():
             external_metadata = JobExternalOutputMetadataWrapper( job )