# HG changeset patch
# User devteam
# Date 1437508860 14400
# Node ID 8afd8a379d5f086f22ceb1f0723c0bad9485781b
# Parent  6eaefb5f755acb8ad3126395d96d3e8828f92b1f
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

diff -r 6eaefb5f755a -r 8afd8a379d5f tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 17 11:23:25 2014 -0500
+++ b/tool_dependencies.xml	Tue Jul 21 16:01:00 2015 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie" version="0.12.7">
-      <repository changeset_revision="028d22e7b70f" name="package_bowtie_0_12_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="tophat" version="1.4.0">
-      <repository changeset_revision="0fea0c8cc6cf" name="package_tophat_1_4_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="0fea0c8cc6cf" name="package_tophat_1_4_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 6eaefb5f755a -r 8afd8a379d5f tophat_wrapper.xml
--- a/tophat_wrapper.xml	Mon Nov 17 11:23:25 2014 -0500
+++ b/tophat_wrapper.xml	Tue Jul 21 16:01:00 2015 -0400
@@ -560,4 +560,7 @@
   --min-segment-intron              The minimum intron length that may be found during split-segment search. The default is 50.
   --max-segment-intron              The maximum intron length that may be found during split-segment search. The default is 500000.
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp120</citation>
+    </citations>
 </tool>