From f7cfc540bd70a696a11e703ac49f19593dd67613 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 4 Jun 2012 09:29:51 -0400
Subject: [PATCH] Clarify inputs for forward, reverse reads in Tophat2 wrapper.

---
 tools/ngs_rna/tophat2_wrapper.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index 69d0b37c934..a03eceeab8d 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -124,8 +124,8 @@
                 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
             </when>
             <when value="paired">
-                <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
-                <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+                <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+                <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" />
                 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs"  help="The standard deviation for the distribution on inner distances between mate pairs."/>
                 <!-- Discordant pairs. -->