# HG changeset patch
# User jjohnson
# Date 1462303091 14400
# Node ID 4fe2e80d4ae13ad4a69b7963fd6c38d6f3125850
# Parent  b22f8634ff847f8e5889d46ad7b6a2c432392cc3
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 0eb27e6896eacbb49a979fa4b34c31859e7fb1a8-dirty

diff -r b22f8634ff84 -r 4fe2e80d4ae1 defuse.xml
--- a/defuse.xml	Sun Jan 17 14:11:06 2016 -0500
+++ b/defuse.xml	Tue May 03 15:18:11 2016 -0400
@@ -84,10 +84,10 @@
       <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
     </when> <!-- full -->
   </conditional>  <!-- defuse_param -->
-  <param name="breakpoints_bam" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
+  <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
   <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <stdio>
diff -r b22f8634ff84 -r 4fe2e80d4ae1 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jan 17 14:11:06 2016 -0500
+++ b/tool_dependencies.xml	Tue May 03 15:18:11 2016 -0400
@@ -16,7 +16,7 @@
         <repository changeset_revision="cc0f4b49b6f1" name="package_blat_35x1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="ada" version="2.0.3">
         <repository changeset_revision="f0e6af8a95e5" name="package_r_ada_2_0_3" owner="jjohnson" toolshed="https://toolshed.g2.bx.psu.edu" />