# HG changeset patch
# User portiahollyoak
# Date 1463995162 14400
# Node ID 8fee2dac93a436fb0b38e80dc32e37e0c49a6de2
# Parent  2de4be065de4e9bdfcb585026f0794497336b250
planemo upload for repository https://github.com/portiahollyoak/Tools commit f09b05c40adb6e529fc461466ee67bf41c3a552f

diff -r 2de4be065de4 -r 8fee2dac93a4 breakdancermax.xml
--- a/breakdancermax.xml	Fri May 20 04:59:47 2016 -0400
+++ b/breakdancermax.xml	Mon May 23 05:19:22 2016 -0400
@@ -33,7 +33,7 @@
         $copy_number_bam
         $allele_freq
         -y "$output_score_filter"
-         output_config_file &&
+         output_config_file > "$breakdancer_stdout" &&
         mv "$sample_name" "$results_bed"
     ]]></command>
     <inputs>
@@ -64,7 +64,8 @@
         <param name="output_score_filter" type="integer" value="30" label="Output Score filter"/>
     </inputs>
     <outputs>
-        <data name="results_bed" type="data" format="bed" help="BED file containing SVs and supporting reads" label="${sample_name}"/>
+        <data name="results_bed" type="data" format="bed" label="${sample_name} Breakdancer BED file containing SVs and supporting reads "/>
+        <data name="results_stdout" type="data" format="bed" label="${sample_name} Breakdancer summary"/>
     </outputs>
     <tests>
         <test>