diff picard_SamToFastq.xml @ 7:08f69add4d06 draft

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

--- a/picard_SamToFastq.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_SamToFastq.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,13 +4,13 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
      
-    echo "BAM" > $report &amp;&amp;    ## This is necessary for output dataset detection (see output tags below)
+    echo "BAM" > $report &&    ## This is necessary for output dataset detection (see output tags below)
     
     @java_options@
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     SamToFastq
     
     INPUT="${inputFile}"
@@ -50,7 +50,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -100,9 +100,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>