The filter on the tophat2  fusions output wasn't being evaluated correctly when 
settingsType is preSet since the param dict wouldn't then have an entry for 

$ hg diff tools/ngs_rna/tophat2_wrapper.xml
diff -r 3f12146d6d81 tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 14:10:56 2012 -0400
+++ b/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 15:47:47 2012 -0500
@@ -297,7 +297,7 @@

         <data format="tabular" name="fusions" label="${} on ${on_string}: fusions" 
-            <filter>(params['fusion_search']['do_search'] == 'Yes')</filter>
+            <filter>(params['settingsType'] == 'full' and 
params['fusion_search']['do_search'] == 'Yes')</filter>
         <data format="bed" name="insertions" label="${} on ${on_string}: 
insertions" from_work_dir="tophat_out/insertions.bed">

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