diff picard_AddOrReplaceReadGroups.xml @ 15:a5a13ea16d17 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a

--- a/picard_AddOrReplaceReadGroups.xml	Mon Apr 16 21:27:09 2018 -0400
+++ b/picard_AddOrReplaceReadGroups.xml	Tue Jun 19 11:28:30 2018 -0400
@@ -3,10 +3,10 @@
   <macros>
     <import>picard_macros.xml</import>
     <import>read_group_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@WRAPPER_VERSION@">1</token>
   </macros>
   <expand macro="requirements" />
-  <command detect_errors="exit_code">
+  <command detect_errors="exit_code"><![CDATA[
     @define_read_group_helpers@
     #set $rg_auto_name = $read_group_name_default($inputFile)
     @set_read_group_vars@
@@ -26,9 +26,10 @@
       VALIDATION_STRINGENCY="${validation_stringency}"
       QUIET=true
       VERBOSITY=ERROR
+      @TMPDIR_OPTION@
       OUTPUT="${outFile}"
 
-  </command>
+  ]]></command>
 
   <inputs>
     <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />