diff --git a/lib/galaxy/tools/parser/yaml.py b/lib/galaxy/tools/parser/yaml.py
index f4f05a15c9e..76211d6ff85 100644
--- a/lib/galaxy/tools/parser/yaml.py
+++ b/lib/galaxy/tools/parser/yaml.py
@@ -75,7 +75,7 @@ class YamlToolSource(ToolSource):
         for output in output_defs:
             outputs[output.name] = output
         # TODO: parse outputs collections
-        return output_defs, odict()
+        return outputs, odict()
 
     def _parse_output(self, tool, name, output_dict):
         # TODO: handle filters, actions, change_format
diff --git a/test/functional/tools/disambiguate_cond.xml b/test/functional/tools/disambiguate_cond.xml
index 5279083495d..2465721b6d4 100644
--- a/test/functional/tools/disambiguate_cond.xml
+++ b/test/functional/tools/disambiguate_cond.xml
@@ -38,8 +38,10 @@
                     <when value="true">
                         <param type="data" name="file" />
                     </when>
+                    <when value="false" />
                 </conditional>
             </when>
+            <when value="false" />
         </conditional>               
     </inputs>
     <outputs>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index a3f3a358607..2ad67eff206 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -6,7 +6,6 @@
   <tool file="boolean_conditional.xml" />
   <tool file="composite.xml" />
   <tool file="environment_variables.xml" />
-  <tool file="compare_bam_as_sam.xml" />
   <tool file="code_file.xml" />
   <tool file="disambiguate_cond.xml" />
   <tool file="multi_repeats.xml"/>