From d802171ccb7b93faec603bd17bb60ecaab1e185d Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 6 Jun 2012 14:42:21 -0400
Subject: [PATCH] Update default and help for Tophat2 coverage search
 parameter.

---
 tools/ngs_rna/tophat2_wrapper.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index a03eceeab8d..32f6ed9f9d2 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -231,9 +231,9 @@
           
               <!-- Coverage search. -->
               <conditional name="coverage_search">
-                <param name="use_search" type="select" label="Use Coverage Search">
-                    <option selected="true" value="Yes">Yes</option>
-                    <option value="No">No</option>
+                <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
+                    <option selected="true" value="No">No</option>
+                    <option value="Yes">Yes</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" />