--- a/picard_MarkDuplicates.xml	Wed Nov 11 12:23:17 2015 -0500
+++ b/picard_MarkDuplicates.xml	Sun Nov 27 15:11:50 2016 -0500
@@ -4,33 +4,33 @@
     <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
     MarkDuplicates
-    
+
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
-    
+
     METRICS_FILE="${metrics_file}"
     #for $element in $comments:
       COMMENT="${element.comment}"
     #end for
     REMOVE_DUPLICATES="${remove_duplicates}"
     ASSUME_SORTED="${assume_sorted}"
-    
+
     DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
-    
+
     #import pipes
     READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
-  </command>
+
+  ]]></command>
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
@@ -54,14 +54,14 @@
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
    <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
@@ -72,14 +72,11 @@
       <param name="optical_duplicate_pixel_distance" value="100"/>
       <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <help>
 
 **Purpose**
@@ -90,34 +87,34 @@
 
 @description@
 
-  COMMENT=String  
-  CO=String                     Comment(s) to include in the output file's header.  This option may be specified 0 or 
-                                more times. 
+  COMMENT=String
+  CO=String                     Comment(s) to include in the output file's header.  This option may be specified 0 or
+                                more times.
+
+  REMOVE_DUPLICATES=Boolean     If true do not write duplicates to the output file instead of writing them with
+                                appropriate flags set.  Default value: false.
 
-  REMOVE_DUPLICATES=Boolean     If true do not write duplicates to the output file instead of writing them with 
-                                appropriate flags set.  Default value: false.  
-  
-  READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read 
-                                names are parsed to extract three variables: tile/region, x coordinate and y coordinate. 
-                                These values are used to estimate the rate of optical duplication in order to give a more 
-                                accurate estimated library size. Set this option to null to disable optical duplicate 
-                                detection. The regular expression should contain three capture groups for the three 
-                                variables, in order. It must match the entire read name. Note that if the default regex 
-                                is specified, a regex match is not actually done, but instead the read name  is split on 
-                                colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be 
-                                tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements 
-                                are assumed to be tile, x and y values.  Default value: 
+  READ_NAME_REGEX=String        Regular expression that can be used to parse read names in the incoming SAM file. Read
+                                names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
+                                These values are used to estimate the rate of optical duplication in order to give a more
+                                accurate estimated library size. Set this option to null to disable optical duplicate
+                                detection. The regular expression should contain three capture groups for the three
+                                variables, in order. It must match the entire read name. Note that if the default regex
+                                is specified, a regex match is not actually done, but instead the read name  is split on
+                                colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
+                                tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
+                                are assumed to be tile, x and y values.  Default value:
                                 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
-                                
+
   DUPLICATE_SCORING_STRATEGY=ScoringStrategy
-  DS=ScoringStrategy            The scoring strategy for choosing the non-duplicate among candidates.  Default value: 
-                                SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} 
-  
+  DS=ScoringStrategy            The scoring strategy for choosing the non-duplicate among candidates.  Default value:
+                                SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
+
   OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
-                                The maximum offset between two duplicte clusters in order to consider them optical 
-                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) 
-                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in 
-                                which case 50-100 is more normal.  Default value: 100. 
+                                The maximum offset between two duplicte clusters in order to consider them optical
+                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
+                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
+                                which case 50-100 is more normal.  Default value: 100.
 
 @more_info@