diff picard_FixMateInformation.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

--- a/picard_FixMateInformation.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_FixMateInformation.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,10 +4,10 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     FixMateInformation
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -19,7 +19,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
@@ -39,13 +39,10 @@
       <param name="add_mate_cigar" value="True"/>
       <param name="assume_sorted" value="False"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>