# HG changeset patch
# User bioitcore
# Date 1505240000 14400
# Node ID 27d8ed0146620765d878e47939552d7a382d9c71
# Parent  ec38f053b647d803c397f57e4e544ac25fbb787e
planemo upload commit 93e677982c3636da455de2f827a87e516c7985ac-dirty

diff -r ec38f053b647 -r 27d8ed014662 chimerascan.xml
--- a/chimerascan.xml	Tue Sep 12 13:59:07 2017 -0400
+++ b/chimerascan.xml	Tue Sep 12 14:13:20 2017 -0400
@@ -1,13 +1,15 @@
 <tool id="chimerascan" name="ChimeraScan">
     <description>A tool for identifying chimeric transcription in sequencing data.</description>
-    <command detect_errors="exit_code">
-            bash $__tool_directory__/run.sh && python $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex 
+    <command detect_errors="exit_code"><![CDATA[
+            bash $__tool_directory__/run.sh &&
+            python $__tool_directory__/chimerascan_run.py -p 8 $__tool_directory__/myindex
             #if $input_type_conditional.chimerascan_input_type == "paired"
                     $input_type_conditional.input_1 $input_type_conditional.input_2
             #else
                     $input_type_conditional.input.forward $input_type_conditional.input.reverse
             #end if
             $galaxy_output
+    ]]>
     </command>
     <inputs>
         <conditional name="input_type_conditional">