Fix errors when starting "./run_tests.sh -with_framework_test_tools -api"

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

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>

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"/>