# HG changeset patch
# User devteam
# Date 1480277496 18000
# Node ID 08f69add4d06c87416277d2246a3ca0b841394db
# Parent  961236c5ec736638e5d34118ccb9feb64a8ae2bd
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

diff -r 961236c5ec73 -r 08f69add4d06 picard_AddCommentsToBam.xml
--- a/picard_AddCommentsToBam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_AddCommentsToBam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,9 +4,9 @@
     <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
       AddCommentsToBam
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -16,8 +16,8 @@
       QUIET=true
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
-  </command>
-  
+  ]]></command>
+
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
     <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
@@ -31,11 +31,8 @@
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
   </outputs>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <tests>
   <test>
       <param name="inputFile" value="picard_AddCommentsToBam.bam" />
@@ -57,7 +54,7 @@
 @description@
 
   COMMENT=String
-  C=String          Comments to add to the BAM file  This option may be specified 0 or more times. 
+  C=String          Comments to add to the BAM file  This option may be specified 0 or more times.
 
 @more_info@
   </help>
diff -r 961236c5ec73 -r 08f69add4d06 picard_AddOrReplaceReadGroups.xml
--- a/picard_AddOrReplaceReadGroups.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_AddOrReplaceReadGroups.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -5,12 +5,12 @@
     <import>read_group_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code">
     @define_read_group_helpers@
     #set $rg_auto_name = $read_group_name_default($inputFile)
     @set_read_group_vars@
     @java_options@
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
       AddOrReplaceReadGroups
       INPUT="${inputFile}"
       $format_read_group("RGLB=", $rg_lb, '"')
@@ -39,9 +39,6 @@
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
   </outputs>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <tests>
     <test>
diff -r 961236c5ec73 -r 08f69add4d06 picard_BedToIntervalList.xml
--- a/picard_BedToIntervalList.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_BedToIntervalList.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
     
-    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
+    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
        
     #if str( $reference_source.reference_source_selector ) == "history":
         
-      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
       
-      &amp;&amp;
+      &&
       
     #else:
     
@@ -27,7 +27,7 @@
     
     #end if 
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
       BedToIntervalList
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -36,7 +36,7 @@
       QUIET=true
       VERBOSITY=ERROR
       
-  </command>
+  ]]></command>
   
   <inputs>
     
@@ -71,13 +71,10 @@
       <param name="reference_source_selector" value="history" />
       <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
       <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
-      <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" />
+      <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" />
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_CleanSam.xml
--- a/picard_CleanSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CleanSam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,16 +4,16 @@
     <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
     CleanSam
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
     QUIET=true
     VERBOSITY=ERROR
     VALIDATION_STRINGENCY=${validation_stringency}
-  </command>
+  ]]></command>
   
   <inputs>
     <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -27,9 +27,6 @@
     </data>
   </outputs>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <tests>
     <test>
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectAlignmentSummaryMetrics.xml
--- a/picard_CollectAlignmentSummaryMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,22 +4,19 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
 
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
 
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     CollectAlignmentSummaryMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -40,7 +37,7 @@
     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."/>
     <conditional name="reference_source">
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectBaseDistributionByCycle.xml
--- a/picard_CollectBaseDistributionByCycle.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectBaseDistributionByCycle.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     CollectBaseDistributionByCycle
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -32,7 +32,7 @@
     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."/>
     <conditional name="reference_source">
@@ -76,9 +76,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectGcBiasMetrics.xml
--- a/picard_CollectGcBiasMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectGcBiasMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
-    java -jar \$JAVA_JAR_PATH/picard.jar
+
+    picard
     CollectGcBiasMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -29,12 +29,12 @@
     IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     ASSUME_SORTED="${assume_sorted}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
-  </command>
+
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
     <conditional name="reference_source">
@@ -55,19 +55,19 @@
     </conditional>
     <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/>
     <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/>
-    <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> 
+    <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
     <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="window_size" value="100" />
@@ -78,13 +78,10 @@
       <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" />
       <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" />
       <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test> 
+    </test>
   </tests>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <help>
 
 .. class:: infomark
@@ -97,15 +94,15 @@
 
 @description@
 
-  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value: 
-                                false. Possible values: {true, false} 
+  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
+                                false. Possible values: {true, false}
 
-  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false. 
-                                This option can be set to 'null' to clear the default value. Possible values: {true, 
-                                false} 
+  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
+                                This option can be set to 'null' to clear the default value. Possible values: {true,
+                                false}
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True
 
 @more_info@
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectInsertSizeMetrics.xml
--- a/picard_CollectInsertSizeMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectInsertSizeMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     CollectInsertSizeMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -38,7 +38,7 @@
     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."/>
     <conditional name="reference_source">
@@ -91,9 +91,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectRnaSeqMetrics.xml
--- a/picard_CollectRnaSeqMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,9 +4,9 @@
         <import>picard_macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.1.2">R</requirement>
+        <requirement type="package" version="3.3.1">r</requirement>
     </expand>
-    <command>
+    <command detect_errors="exit_code"><![CDATA[
 
       ## Set up input files
       
@@ -15,7 +15,7 @@
       #set $reference_fasta_filename = "localref.fa"
     
       #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
       #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
       #end if
@@ -23,12 +23,12 @@
       ## refFlat data
       ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
       
-      grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &amp;&amp;
+      grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
       
       ## Start picard command
       
       @java_options@
-      java -jar \$JAVA_JAR_PATH/picard.jar
+      picard
       CollectRnaSeqMetrics
       REF_FLAT=refFlat.tab
       
@@ -55,7 +55,7 @@
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
     
-   </command>
+   ]]></command>
    
    <inputs>
       <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
@@ -77,7 +77,7 @@
       <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help" />
       <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>
       <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">
-	 <option value="NONE" select="True">None</option>
+	 <option value="NONE" selected="True">None</option>
 	 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
 	 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
       </param>
@@ -102,9 +102,6 @@
       <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
   </outputs>
   
-   <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   <tests>
     <test>
       <param name="reference_source_selector" value="history"/>
diff -r 961236c5ec73 -r 08f69add4d06 picard_CollectWgsMetrics.xml
--- a/picard_CollectWgsMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectWgsMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,19 +4,19 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     CollectWgsMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -29,7 +29,7 @@
     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"/>
     <conditional name="reference_source">
@@ -73,9 +73,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_DownsampleSam.xml
--- a/picard_DownsampleSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_DownsampleSam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,10 +4,9 @@
     <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
     DownsampleSam
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -16,7 +15,7 @@
       QUIET=true
       VERBOSITY=ERROR
       VALIDATION_STRINGENCY=${validation_stringency}
-  </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 or BAM dataset" />
     <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
@@ -26,9 +25,6 @@
     
   </inputs>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <outputs>
     <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
diff -r 961236c5ec73 -r 08f69add4d06 picard_EstimateLibraryComplexity.xml
--- a/picard_EstimateLibraryComplexity.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_EstimateLibraryComplexity.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
     EstimateLibraryComplexity
     
     INPUT="${inputFile}"
@@ -25,7 +25,7 @@
     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" />
     <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU; default=5"/>
@@ -63,9 +63,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_FastqToSam.xml
--- a/picard_FastqToSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_FastqToSam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,13 +4,10 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     FastqToSam
     
     #if str( $input_type.input_type_selector ) == "se":
@@ -70,7 +67,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <conditional name="input_type">
       <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
diff -r 961236c5ec73 -r 08f69add4d06 picard_FilterSamReads.xml
--- a/picard_FilterSamReads.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_FilterSamReads.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,12 +4,12 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
     ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     SortSam
     INPUT="${inputFile}"
     OUTPUT=query_sorted_bam.bam
@@ -18,9 +18,9 @@
     QUIET=true
     VERBOSITY=ERROR
     
-    &amp;&amp;
+    &&
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     FilterSamReads
     INPUT=query_sorted_bam.bam
     FILTER="${filter_type.filter}"
@@ -35,7 +35,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <conditional name="filter_type">
@@ -69,20 +69,17 @@
       <param name="filter" value="includeReadList"/>
       <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
     <test>
       <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
       <param name="filter" value="excludeReadList"/>
       <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_FixMateInformation.xml
--- 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>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_MarkDuplicates.xml
--- a/picard_MarkDuplicates.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_MarkDuplicates.xml	Sun Nov 27 15:11:36 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@
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_MarkDuplicatesWithMateCigar.xml
--- a/picard_MarkDuplicatesWithMateCigar.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_MarkDuplicatesWithMateCigar.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
     MarkDuplicatesWithMateCigar
     
     INPUT="${inputFile}"
@@ -35,7 +35,7 @@
     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"/>
       <param name="comment" type="text" label="Add this comment to BAM dataset"/>
@@ -46,7 +46,7 @@
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
 
     <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=TOTAL_MAPPED_REFERENCE_LENGTH">
-      <option value="TOTAL_MAPPED_REFERENCE_LENGTH" select="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
+      <option value="TOTAL_MAPPED_REFERENCE_LENGTH" selected="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>
       <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
     </param>
 
@@ -84,9 +84,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_MeanQualityByCycle.xml
--- a/picard_MeanQualityByCycle.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_MeanQualityByCycle.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     MeanQualityByCycle
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -33,7 +33,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
     <conditional name="reference_source">
@@ -77,9 +77,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_MergeBamAlignment.xml
--- a/picard_MergeBamAlignment.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_MergeBamAlignment.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,20 +4,20 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
     
-    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
+    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
        
     #if str( $reference_source.reference_source_selector ) == "history":
         
-      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
       
-      &amp;&amp;
+      &&
       
     #else:
     
@@ -25,7 +25,7 @@
     
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     MergeBamAlignment
       UNMAPPED_BAM="${unmapped_bam}"
       
@@ -85,7 +85,7 @@
       QUIET=true
       VERBOSITY=ERROR
       
-  </command>
+  ]]></command>
   
   <inputs>
     
@@ -194,13 +194,10 @@
       <param name="clip_overlapping_reads" value="True"/>
       <param name="include_secondary_alignments" value="True"/>
       <param name="add_mate_cigar" value="True"/>
-      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_MergeSamFiles.xml
--- a/picard_MergeSamFiles.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_MergeSamFiles.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
     MergeSamFiles
     
     #for $element in $inputFile:
@@ -28,7 +28,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
@@ -52,13 +52,10 @@
       <param name="assume_sorted" value="False"/>
       <param name="merge_sequence_dictionaries" value="False"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_NormalizeFasta.xml
--- a/picard_NormalizeFasta.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_NormalizeFasta.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,15 +4,15 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
   
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa  
     #set $fasta_file="local_fasta.fa"
-    ln -s "${inputFile}" "${fasta_file}" &amp;&amp;    
+    ln -s "${inputFile}" "${fasta_file}" &&    
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     NormalizeFasta
     
     INPUT="${fasta_file}"
@@ -23,7 +23,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
     <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
@@ -43,9 +43,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_QualityScoreDistribution.xml
--- a/picard_QualityScoreDistribution.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_QualityScoreDistribution.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
     
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     QualityScoreDistribution
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -34,7 +34,7 @@
     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"/>
     <conditional name="reference_source">
@@ -80,9 +80,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_ReorderSam.xml
--- a/picard_ReorderSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_ReorderSam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,20 +4,20 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     #set $picard_dict = "localref.dict"
     #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension
     
-    ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp;
+    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
        
     #if str( $reference_source.reference_source_selector ) == "history":
         
-      java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
+      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
       QUIET=true
       VERBOSITY=ERROR
       
-      &amp;&amp;
+      &&
       
     #else:
     
@@ -25,7 +25,7 @@
     
     #end if
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     ReorderSam
       INPUT="${inputFile}"
       OUTPUT="${outFile}"
@@ -37,7 +37,7 @@
       QUIET=true
       VERBOSITY=ERROR
       
-  </command>
+  ]]></command>
   
   <inputs>
     
@@ -76,13 +76,10 @@
       <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
       <param name="allow_incomplete_dict_concordance" value="false"/>
       <param name="allow_contig_length_discordance" value="false"/>
-      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_ReplaceSamHeader.xml
--- a/picard_ReplaceSamHeader.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_ReplaceSamHeader.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,15 +4,15 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @java_options@
     
   
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa  
     #set $fasta_file="local_fasta.fa"
-    ln -s "${inputFile}" "${fasta_file}" &amp;&amp;    
+    ln -s "${inputFile}" "${fasta_file}" &&    
     
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     ReplaceSamHeader
     
     INPUT="${inputFile}"
@@ -22,7 +22,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
@@ -40,9 +40,6 @@
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml
--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.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
     RevertOriginalBaseQualitiesAndAddMateCigar
     
     INPUT="${inputFile}"
@@ -21,7 +21,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
@@ -41,13 +41,10 @@
       <param name="restore_original_qualities" value="True"/>
       <param name="max_records_to_examine" value="10000"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_RevertSam.xml
--- a/picard_RevertSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_RevertSam.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
     RevertSam
     
     INPUT="${inputFile}"
@@ -31,7 +31,7 @@
     QUIET=true
     VERBOSITY=ERROR
   
-  </command>
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
@@ -70,13 +70,10 @@
       <param name="library_name" value="null"/>
       <param name="sort_order" value="coordinate"/>
       <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
   
   <help>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_SamToFastq.xml
--- 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>
 
diff -r 961236c5ec73 -r 08f69add4d06 picard_SortSam.xml
--- a/picard_SortSam.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_SortSam.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,44 +4,64 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
+    #if $sort_order == "queryname":
+        #set $output = "output.sam"
+        ln -s '${outFile}' output.sam &&
+    #else:
+        #set $output = $outFile
+    #end if
     @java_options@
-    java -jar \$JAVA_JAR_PATH/picard.jar
+    picard
     SortSam
     INPUT="${inputFile}"
-    OUTPUT="${outFile}"
+    OUTPUT='${output}'
     SORT_ORDER="${sort_order}"
     QUIET=true
     VERBOSITY=ERROR
     VALIDATION_STRINGENCY=${validation_stringency}
-  </command>
-  
+  ]]></command>
+
   <inputs>
     <param name="inputFile" 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="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
+    <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.">
       <option value="coordinate" selected="True">Coordinate</option>
       <option value="queryname">Queryname</option>
     </param>
     <expand macro="VS" />
   </inputs>
-  
+
   <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
+      <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
+          <change_format>
+              <when input="sort_order" value="queryname" format="sam"/>
+          </change_format>
     </data>
   </outputs>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <tests>
+      <!-- This test fails when setting metadata on non-coordinate sorted bam files.
+           This should be handled better in Galaxy (info as of release 16.0).
+           Workaroudn is to produce queryname sorted sam files.
     <test>
       <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
       <param name="sort_order" value="queryname"/>
-      <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
+      <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
+    </test>
+  -->
+    <test>
+      <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
+      <param name="sort_order" value="queryname"/>
+      <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
+    </test>
+    <test>
+      <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
+      <param name="sort_order" value="coordinate"/>
+      <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
+
   <help>
 
 .. class:: infomark
@@ -56,7 +76,7 @@
 
   SORT_ORDER=SortOrder
   SO=SortOrder          Sort order of output file. You can either sort by queryname or by coordinate.
- 
+
  @more_info@
 
   </help>
diff -r 961236c5ec73 -r 08f69add4d06 picard_ValidateSamFile.xml
--- a/picard_ValidateSamFile.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_ValidateSamFile.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,49 +4,52 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
-  <command>
-    
+  <stdio>
+    <exit_code range="1:"  level="warning"/>
+  </stdio>
+  <command><![CDATA[
+
     ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
-    
-    [ `ulimit -Hn` = unlimited ] &amp;&amp; ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
-    
-    &amp;&amp;
-    
+
+    [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
+
+    &&
+
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
+
     @java_options@
-    
-    java -jar \$JAVA_JAR_PATH/picard.jar
+
+    picard
     ValidateSamFile
-    
+
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
     MODE="${mode}"
-    
+
     #if str( $ignore ) != "None":
       #for $element in str( $ignore ).split(','):   ## See trello card https://trello.com/c/9nW02Zhd
         IGNORE="${element}"
       #end for
     #end if
-    
+
     MAX_OUTPUT="${max_output}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     IGNORE_WARNINGS="${ignore_warnings}"
     IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
     MAX_OPEN_TEMP_FILES=`ulimit -Sn`
-     
+
     VERBOSITY=ERROR
     QUIET=true
-   
-  </command>
+
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />
      <conditional name="reference_source">
@@ -63,11 +66,11 @@
           <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
         </param>
       </when>
-      <when value="history"> 
+      <when value="history">
         <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
       </when>
     </conditional>
-     
+
     <param name="mode" type="select" label="Select output mode" help="MODE">
       <option value="VERBOSE">Verbose</option>
       <option value="SUMMARY">Summary</option>
@@ -135,13 +138,13 @@
     <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
     <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
     <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/>
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
@@ -156,11 +159,7 @@
       <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
     </test>
   </tests>
-  
-  <stdio>
-    <exit_code range="1:"  level="warning"/>
-  </stdio>
-  
+
   <help>
 
 **Purpose**
@@ -172,52 +171,52 @@
 @description@
 
   MODE=Mode
-  M=Mode                        Mode of output  Default value: VERBOSE. This option can be set to 'null' to clear the 
-                                default value. Possible values: {VERBOSE, SUMMARY} 
-  
-  IGNORE=Type                   List of validation error types to ignore.  Possible values: {INVALID_QUALITY_FORMAT, 
-                                INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, 
-                                INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, 
-                                INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, 
-                                INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, 
-                                INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, 
-                                ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, 
-                                INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, 
-                                MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, 
-                                MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, 
-                                READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, 
-                                MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, 
-                                MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, 
-                                MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, 
-                                E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, 
-                                POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, 
-                                HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, 
-                                INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, 
-                                DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, 
-                                DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, 
-                                MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be 
-                                specified 0 or more times. 
-  
+  M=Mode                        Mode of output  Default value: VERBOSE. This option can be set to 'null' to clear the
+                                default value. Possible values: {VERBOSE, SUMMARY}
+
+  IGNORE=Type                   List of validation error types to ignore.  Possible values: {INVALID_QUALITY_FORMAT,
+                                INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
+                                INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
+                                INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
+                                INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
+                                INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
+                                ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
+                                INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
+                                MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
+                                MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
+                                READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
+                                MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
+                                MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
+                                MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
+                                E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
+                                POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
+                                HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
+                                INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
+                                DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
+                                DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
+                                MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
+                                specified 0 or more times.
+
   MAX_OUTPUT=Integer
-  MO=Integer                    The maximum number of lines output in verbose mode  Default value: 100. This option can 
-                                be set to 'null' to clear the default value. 
-  
+  MO=Integer                    The maximum number of lines output in verbose mode  Default value: 100. This option can
+                                be set to 'null' to clear the default value.
+
   REFERENCE_SEQUENCE=File
-  R=File                        Reference sequence file, the NM tag check will be skipped if this is missing  Default 
-                                value: null. 
-  
-  IGNORE_WARNINGS=Boolean       If true, only report errors and ignore warnings.  Default value: false. This option can 
-                                be set to 'null' to clear the default value. Possible values: {true, false} 
-  
-  VALIDATE_INDEX=Boolean        If true and input is a BAM file with an index file, also validates the index.  Default 
-                                value: true. This option can be set to 'null' to clear the default value. Possible 
-                                values: {true, false} 
-  
+  R=File                        Reference sequence file, the NM tag check will be skipped if this is missing  Default
+                                value: null.
+
+  IGNORE_WARNINGS=Boolean       If true, only report errors and ignore warnings.  Default value: false. This option can
+                                be set to 'null' to clear the default value. Possible values: {true, false}
+
+  VALIDATE_INDEX=Boolean        If true and input is a BAM file with an index file, also validates the index.  Default
+                                value: true. This option can be set to 'null' to clear the default value. Possible
+                                values: {true, false}
+
   IS_BISULFITE_SEQUENCED=Boolean
-  BISULFITE=Boolean             Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not 
-                                counted as an error in computing the value of the NM tag.  Default value: false. This 
-                                option can be set to 'null' to clear the default value. Possible values: {true, false} 
-  
+  BISULFITE=Boolean             Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
+                                counted as an error in computing the value of the NM tag.  Default value: false. This
+                                option can be set to 'null' to clear the default value. Possible values: {true, false}
+
 @more_info@
 
   </help>
diff -r 961236c5ec73 -r 08f69add4d06 picard_macros.xml
--- a/picard_macros.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_macros.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -7,20 +7,20 @@
         </param>
     </xml>
 
-    <token name="@TOOL_VERSION@">1.136</token>
+    <token name="@TOOL_VERSION@">2.7.1</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.136">picard</requirement>
+            <requirement type="package" version="2.7.1">picard</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@java_options@">
-    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &amp;&amp;
-    export _JAVA_OPTIONS &amp;&amp;
-    </token>
-    
+    <token name="@java_options@"><![CDATA[
+    _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
+    export _JAVA_OPTIONS &&
+    ]]></token>
+
     <token name="@more_info@">
 ------
 
@@ -28,7 +28,7 @@
 
 Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/.
     </token>
-    
+
 
     <token name="@description@">
 ------
@@ -49,7 +49,7 @@
 
 .. csv-table::
    :header-rows: 1
-    
+
     Tag,Importance,Definition,Meaning
     "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number.  Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came.  Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
     "SM","Sample. Use pool name where a pool is being sequenced.","Required.  As important as ID.","The name of the sample sequenced in this read group.  GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample.  Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
@@ -65,13 +65,13 @@
  @RG     ID:FLOWCELL1.LANE2      PL:illumina     LB:LIB-DAD-1 SM:DAD      PI:200
  @RG     ID:FLOWCELL1.LANE3      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
  @RG     ID:FLOWCELL1.LANE4      PL:illumina     LB:LIB-DAD-2 SM:DAD      PI:400
-  
+
  Mom's data:
  @RG     ID:FLOWCELL1.LANE5      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
  @RG     ID:FLOWCELL1.LANE6      PL:illumina     LB:LIB-MOM-1 SM:MOM      PI:200
  @RG     ID:FLOWCELL1.LANE7      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
  @RG     ID:FLOWCELL1.LANE8      PL:illumina     LB:LIB-MOM-2 SM:MOM      PI:400
- 
+
  Kid's data:
  @RG     ID:FLOWCELL2.LANE1      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
  @RG     ID:FLOWCELL2.LANE2      PL:illumina     LB:LIB-KID-1 SM:KID      PI:200
@@ -89,6 +89,6 @@
 
 
     </token>
-    
+
 
 </macros>
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_CASM_test1.tab
--- a/test-data/picard_CASM_test1.tab	Mon Nov 09 11:49:09 2015 -0500
+++ b/test-data/picard_CASM_test1.tab	Sun Nov 27 15:11:36 2016 -0500
@@ -1,12 +1,12 @@
 ## htsjdk.samtools.metrics.StringHeader
-# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=None] IS_BISULFITE_SEQUENCED=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_639.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=localref.fa INPUT=/tmp/tmppFEHK6/files/000/dataset_1.dat OUTPUT=/tmp/tmppFEHK6/files/000/dataset_3.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Thu Oct 02 13:35:09 EDT 2014
+# Started on: Sun Nov 27 10:07:49 CET 2016
 
 ## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
 CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	SAMPLE	LIBRARY	READ_GROUP
-FIRST_OF_PAIR	100	100	1	0	100	1	17831	100	17831	16865	1	0.008188	0.008188	0	251	99	0.99	0	0.46	0	0			
-SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008879	0.008879	0	251	99	1	0	0.545455	0	0			
-PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008534	0.008534	0	251	198	0.994975	0	0.502513	0	0			
+FIRST_OF_PAIR	100	100	1	0	100	1	17831	100	17831	16865	1	0.008132	0.008132	0	251	99	0.99	0	0.46	0.74	0			
+SECOND_OF_PAIR	100	100	1	0	99	0.99	17907	99	17907	16887	1	0.008824	0.008824	0	251	99	1	0	0.545455	0.676768	0			
+PAIR	200	200	1	0	199	0.995	35738	199	35738	33752	1	0.008479	0.008479	0	251	198	0.994975	0	0.502513	0.708543	0			
 
 
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_CollectGcBiasMetrics_test1.tab
--- a/test-data/picard_CollectGcBiasMetrics_test1.tab	Mon Nov 09 11:49:09 2015 -0500
+++ b/test-data/picard_CollectGcBiasMetrics_test1.tab	Sun Nov 27 15:11:36 2016 -0500
@@ -1,48 +1,110 @@
 ## htsjdk.samtools.metrics.StringHeader
-# picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=localref.fa INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_707.dat CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_708.dat SUMMARY_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_706.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 ASSUME_SORTED=true IS_BISULFITE_SEQUENCED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_5.dat SUMMARY_OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_3.dat SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/tmp/tmp_TYiPX/files/000/dataset_1.dat OUTPUT=/tmp/tmp_TYiPX/files/000/dataset_4.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Sat Oct 04 11:22:58 EDT 2014
+# Started on: Sun Nov 27 10:39:24 CET 2016
 
 ## METRICS CLASS	picard.analysis.GcBiasDetailMetrics
-GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH
-24	2	0	0	0	0
-25	15	0	0	0	0
-26	13	0	0	0	0
-27	18	0	0	0	0
-28	50	5	21	4.843529	2.166092
-29	47	0	0	0	0
-30	63	0	0	0	0
-31	97	4	20	1.997332	0.998666
-32	167	3	23	0.870095	0.50235
-33	178	4	22	1.088434	0.544217
-34	225	8	22	1.722144	0.60887
-35	291	5	22	0.832222	0.372181
-36	391	1	21	0.123875	0.123875
-37	506	4	24	0.382888	0.191444
-38	570	0	0	0	0
-39	640	0	0	0	0
-40	729	0	0	0	0
-41	846	1	24	0.057252	0.057252
-42	1060	1	24	0.045694	0.045694
-43	1182	13	22	0.532706	0.147746
-44	1113	8	22	0.348142	0.123087
-45	1161	7	20	0.29203	0.110377
-46	1113	5	20	0.217589	0.097309
-47	1035	8	23	0.374379	0.132363
-48	956	9	23	0.455981	0.151994
-49	913	1	24	0.053051	0.053051
-50	785	5	22	0.308505	0.137968
-51	607	5	22	0.398973	0.178426
-52	436	104	22	11.553373	1.132901
-53	354	13	23	1.778697	0.493322
-54	288	0	0	0	0
-55	232	6	21	1.252637	0.511387
-56	133	0	0	0	0
-57	108	2	24	0.89695	0.634239
-58	65	0	0	0	0
-59	38	0	0	0	0
-60	29	0	0	0	0
-61	10	0	0	0	0
-62	2	0	0	0	0
+ACCUMULATION_LEVEL	GC	WINDOWS	READ_STARTS	MEAN_BASE_QUALITY	NORMALIZED_COVERAGE	ERROR_BAR_WIDTH	SAMPLE	LIBRARY	READ_GROUP
+All Reads	0	0	118	20	0	0			
+All Reads	1	0	0	0	0	0			
+All Reads	2	0	0	0	0	0			
+All Reads	3	0	0	0	0	0			
+All Reads	4	0	0	0	0	0			
+All Reads	5	0	0	0	0	0			
+All Reads	6	0	0	0	0	0			
+All Reads	7	0	0	0	0	0			
+All Reads	8	0	0	0	0	0			
+All Reads	9	0	0	0	0	0			
+All Reads	10	0	0	0	0	0			
+All Reads	11	0	0	0	0	0			
+All Reads	12	0	0	0	0	0			
+All Reads	13	0	0	0	0	0			
+All Reads	14	0	0	0	0	0			
+All Reads	15	0	0	0	0	0			
+All Reads	16	0	0	0	0	0			
+All Reads	17	0	0	0	0	0			
+All Reads	18	0	0	0	0	0			
+All Reads	19	0	0	0	0	0			
+All Reads	20	0	0	0	0	0			
+All Reads	21	0	0	0	0	0			
+All Reads	22	0	0	0	0	0			
+All Reads	23	0	0	0	0	0			
+All Reads	24	2	0	0	0	0			
+All Reads	25	15	0	0	0	0			
+All Reads	26	13	0	0	0	0			
+All Reads	27	18	0	0	0	0			
+All Reads	28	50	5	21	4.843529	2.166092			
+All Reads	29	47	0	0	0	0			
+All Reads	30	63	0	0	0	0			
+All Reads	31	97	4	20	1.997332	0.998666			
+All Reads	32	167	3	23	0.870095	0.50235			
+All Reads	33	178	4	22	1.088434	0.544217			
+All Reads	34	225	8	22	1.722144	0.60887			
+All Reads	35	291	5	22	0.832222	0.372181			
+All Reads	36	391	1	21	0.123875	0.123875			
+All Reads	37	506	4	24	0.382888	0.191444			
+All Reads	38	570	0	0	0	0			
+All Reads	39	640	0	0	0	0			
+All Reads	40	729	0	0	0	0			
+All Reads	41	846	1	24	0.057252	0.057252			
+All Reads	42	1060	1	24	0.045694	0.045694			
+All Reads	43	1182	13	22	0.532706	0.147746			
+All Reads	44	1113	8	22	0.348142	0.123087			
+All Reads	45	1161	7	20	0.29203	0.110377			
+All Reads	46	1113	5	20	0.217589	0.097309			
+All Reads	47	1035	8	23	0.374379	0.132363			
+All Reads	48	956	9	23	0.455981	0.151994			
+All Reads	49	913	1	24	0.053051	0.053051			
+All Reads	50	785	5	22	0.308505	0.137968			
+All Reads	51	607	5	22	0.398973	0.178426			
+All Reads	52	436	104	22	11.553373	1.132901			
+All Reads	53	354	13	23	1.778697	0.493322			
+All Reads	54	288	0	0	0	0			
+All Reads	55	232	6	21	1.252637	0.511387			
+All Reads	56	133	0	0	0	0			
+All Reads	57	108	2	24	0.89695	0.634239			
+All Reads	58	65	0	0	0	0			
+All Reads	59	38	0	0	0	0			
+All Reads	60	29	0	0	0	0			
+All Reads	61	10	0	0	0	0			
+All Reads	62	2	0	0	0	0			
+All Reads	63	0	0	0	0	0			
+All Reads	64	0	0	0	0	0			
+All Reads	65	0	0	0	0	0			
+All Reads	66	0	0	0	0	0			
+All Reads	67	0	0	0	0	0			
+All Reads	68	0	0	0	0	0			
+All Reads	69	0	0	0	0	0			
+All Reads	70	0	0	0	0	0			
+All Reads	71	0	0	0	0	0			
+All Reads	72	0	0	0	0	0			
+All Reads	73	0	0	0	0	0			
+All Reads	74	0	0	0	0	0			
+All Reads	75	0	0	0	0	0			
+All Reads	76	0	0	0	0	0			
+All Reads	77	0	0	0	0	0			
+All Reads	78	0	0	0	0	0			
+All Reads	79	0	0	0	0	0			
+All Reads	80	0	0	0	0	0			
+All Reads	81	0	0	0	0	0			
+All Reads	82	0	0	0	0	0			
+All Reads	83	0	0	0	0	0			
+All Reads	84	0	0	0	0	0			
+All Reads	85	0	0	0	0	0			
+All Reads	86	0	0	0	0	0			
+All Reads	87	0	0	0	0	0			
+All Reads	88	0	0	0	0	0			
+All Reads	89	0	0	0	0	0			
+All Reads	90	0	0	0	0	0			
+All Reads	91	0	0	0	0	0			
+All Reads	92	0	0	0	0	0			
+All Reads	93	0	0	0	0	0			
+All Reads	94	0	0	0	0	0			
+All Reads	95	0	0	0	0	0			
+All Reads	96	0	0	0	0	0			
+All Reads	97	0	0	0	0	0			
+All Reads	98	0	0	0	0	0			
+All Reads	99	0	0	0	0	0			
+All Reads	100	0	0	0	0	0			
 
 
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_CollectWgsMetrics_test1.tab
--- a/test-data/picard_CollectWgsMetrics_test1.tab	Mon Nov 09 11:49:09 2015 -0500
+++ b/test-data/picard_CollectWgsMetrics_test1.tab	Sun Nov 27 15:11:36 2016 -0500
@@ -1,11 +1,11 @@
 ## htsjdk.samtools.metrics.StringHeader
-# picard.analysis.CollectWgsMetrics INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_802.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    STOP_AFTER=-1 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+# picard.analysis.CollectWgsMetrics INPUT=/tmp/tmpOXrG6f/files/000/dataset_1.dat OUTPUT=/tmp/tmpOXrG6f/files/000/dataset_3.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Tue Oct 07 15:46:29 EDT 2014
+# Started on: Sun Nov 27 10:15:01 CET 2016
 
 ## METRICS CLASS	picard.analysis.CollectWgsMetrics$WgsMetrics
-GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_MAPQ	PCT_EXC_DUPE	PCT_EXC_UNPAIRED	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_5X	PCT_10X	PCT_15X	PCT_20X	PCT_25X	PCT_30X	PCT_40X	PCT_50X	PCT_60X	PCT_70X	PCT_80X	PCT_90X	PCT_100X
-16568	2.915983	3.836089	2	2	0	0	0	0	0.008069	0	0.008069	0.240464	0.055831	0.02541	0.011045	0	0	0	0	0	0	0	0	0
+GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_MAPQ	PCT_EXC_DUPE	PCT_EXC_UNPAIRED	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_1X	PCT_5X	PCT_10X	PCT_15X	PCT_20X	PCT_25X	PCT_30X	PCT_40X	PCT_50X	PCT_60X	PCT_70X	PCT_80X	PCT_90X	PCT_100X	HET_SNP_SENSITIVITY	HET_SNP_Q
+16568	2.915862	3.835741	2	2	0	0	0	0.000041	0.008069	0	0.00811	0.684633	0.240464	0.055831	0.02541	0.010985	0	0	0	0	0	0	0	0	0	0.54448	3
 
 ## HISTOGRAM	java.lang.Integer
 coverage	count
@@ -17,8 +17,8 @@
 5	1247
 6	672
 7	468
-8	361
-9	311
+8	362
+9	310
 10	210
 11	95
 12	78
@@ -28,8 +28,8 @@
 16	29
 17	31
 18	53
-19	61
-20	65
+19	62
+20	64
 21	74
 22	32
 23	12
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_DownsampleSam_test1.bam
Binary file test-data/picard_DownsampleSam_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_EstimateLibraryComplexity_test1.tab
--- a/test-data/picard_EstimateLibraryComplexity_test1.tab	Mon Nov 09 11:49:09 2015 -0500
+++ b/test-data/picard_EstimateLibraryComplexity_test1.tab	Sun Nov 27 15:11:36 2016 -0500
@@ -1,11 +1,11 @@
 ## htsjdk.samtools.metrics.StringHeader
-# picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/Users/anton/galaxy-central/database/files/000/dataset_951.dat] OUTPUT=/Users/anton/galaxy-central/database/files/001/dataset_1073.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3472024 CREATE_INDEX=false CREATE_MD5_FILE=false
+# picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/tmp/tmpiSG3kJ/files/000/dataset_1.dat] OUTPUT=/tmp/tmpiSG3kJ/files/000/dataset_2.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
 ## htsjdk.samtools.metrics.StringHeader
-# Started on: Fri Oct 17 13:39:31 EDT 2014
+# Started on: Sun Nov 27 10:17:54 CET 2016
 
 ## METRICS CLASS	picard.sam.DuplicationMetrics
-LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
-Unknown	0	982	0	0	116	0	0.118126	3822
+LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
+Unknown	0	982	0	0	0	116	0	0.118126	3822
 
 ## HISTOGRAM	java.lang.Integer
 duplication_group_count	Unknown
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_FixMateInformation_test1.bam
Binary file test-data/picard_FixMateInformation_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_MarkDuplicates_test1.bam
Binary file test-data/picard_MarkDuplicates_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_MergeBamAlignment_test1.bam
Binary file test-data/picard_MergeBamAlignment_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_MergeBamAlignment_unaligned.bam
Binary file test-data/picard_MergeBamAlignment_unaligned.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam
Binary file test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_SortSam_test1.bam
Binary file test-data/picard_SortSam_test1.bam has changed
diff -r 961236c5ec73 -r 08f69add4d06 test-data/picard_SortSam_test1.sam
diff -r 961236c5ec73 -r 08f69add4d06 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 11:49:09 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="picard" version="1.136">
-        <repository changeset_revision="5fe74a2d3ca7" name="package_picard_1_136" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="R" version="3.1.2">
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>