From 4e4ca2d5424b396dfc13ac97f43c6fbf2e69a266 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Thu, 24 Mar 2011 17:36:06 -0400
Subject: [PATCH] Change default value for Tophat coverage search to true.

---
 tools/ngs_rna/tophat_wrapper.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index fedf0aa45d2..279db09ab58 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -251,8 +251,8 @@
                   <!-- Coverage search. -->
                   <conditional name="coverage_search">
                     <param name="use_search" type="select" label="Use Coverage Search">
-                      <option value="No">No</option>
-                      <option value="Yes">Yes</option>
+                        <option value="Yes">Yes</option>
+                        <option value="No">No</option>
                     </param>
                     <when value="Yes">
                         <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
@@ -357,8 +357,8 @@
                   <!-- Coverage search. -->
                   <conditional name="coverage_search">
                     <param name="use_search" type="select" label="Use Coverage Search">
-                      <option value="No">No</option>
-                      <option value="Yes">Yes</option>
+                        <option value="Yes">Yes</option>
+                        <option value="No">No</option>
                     </param>
                     <when value="Yes">
                         <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />