From 5c3fe000609e1ae0b312b7c8c15ab014776df37e Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 14 Aug 2012 12:17:01 -0400
Subject: [PATCH] Include fusions output in Tophat2 wrapper.

---
 tools/ngs_rna/tophat2_wrapper.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index 7fbfa421e1c..5d258be561f 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -296,6 +296,9 @@
     </inputs>
 
     <outputs>
+        <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
+            <filter>(params['fusion_search']['do_search'] == 'Yes')</filter>
+        </data>
         <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
             <actions>
               <conditional name="refGenomeSource.genomeSource">