# HG changeset patch
# User devteam
# Date 1437502853 14400
# Node ID 04a609b0fdf6f7e9987689770a7029f1feb62f63
# Parent  1cdcaf5fc1da3760aaebc01beabe0ee6de60d6fc
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

diff -r 1cdcaf5fc1da -r 04a609b0fdf6 fastq_trimmer_by_quality.xml
--- a/fastq_trimmer_by_quality.xml	Mon Jan 27 09:26:45 2014 -0500
+++ b/fastq_trimmer_by_quality.xml	Tue Jul 21 14:20:53 2015 -0400
@@ -125,6 +125,8 @@
     </test>
   </tests>
   <help>
+**What it does**
+
 This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends. 
 
 The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found within the sliding window to be used with the user defined comparison operation and comparison value.
@@ -139,10 +141,9 @@
 
 ------
 
-**Citation**
-
-If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
-
 
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq281</citation>
+  </citations>
 </tool>
diff -r 1cdcaf5fc1da -r 04a609b0fdf6 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 27 09:26:45 2014 -0500
+++ b/tool_dependencies.xml	Tue Jul 21 14:20:53 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="galaxy_sequence_utils" version="1.0.0">
-      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="0643676ad5f7" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>