From 46ece42f6e59bf47f26c853ddf44c1675176cb59 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 8 Nov 2011 16:53:19 -0500
Subject: [PATCH] Update FASTQ Groomer tool help to indicate that Illumina 1.8+
 is Sanger encoded.

---
 tools/fastq/fastq_groomer.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/fastq/fastq_groomer.xml b/tools/fastq/fastq_groomer.xml
index 5a3738eb08d..10a4adeb453 100644
--- a/tools/fastq/fastq_groomer.xml
+++ b/tools/fastq/fastq_groomer.xml
@@ -16,7 +16,7 @@
     <param name="input_file" type="data" format="fastq" label="File to groom" />
     <param name="input_type" type="select" label="Input FASTQ quality scores type">
       <option value="solexa">Solexa</option>
-      <option value="illumina">Illumina 1.3+</option>
+      <option value="illumina">Illumina 1.3-1.7</option>
       <option value="sanger" selected="True">Sanger</option>
       <option value="cssanger">Color Space Sanger</option>
     </param>
@@ -358,6 +358,10 @@ When converting between color space (csSanger) and base/sequence space (Sanger,
 
 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
 
+.. class:: infomark
+
+Output from Illumina 1.8+ pipelines are Sanger encoded.
+
 ------
 
 **Citation**