# HG changeset patch
# User devteam
# Date 1481197418 18000
# Node ID 00fe2ff644674f4f1d5ababfa1237b7ee195c418
# Parent  465cbb0cf2ebd6ba93fd29c072ece5ebaab6565e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29

diff -r 465cbb0cf2eb -r 00fe2ff64467 picard_AddOrReplaceReadGroups.xml
--- a/picard_AddOrReplaceReadGroups.xml	Wed Dec 07 14:56:30 2016 -0500
+++ b/picard_AddOrReplaceReadGroups.xml	Thu Dec 08 06:43:38 2016 -0500
@@ -107,17 +107,3 @@
 @more_info@
   </help>
 </tool>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff -r 465cbb0cf2eb -r 00fe2ff64467 picard_CollectRnaSeqMetrics.xml
--- a/picard_CollectRnaSeqMetrics.xml	Wed Dec 07 14:56:30 2016 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Thu Dec 08 06:43:38 2016 -0500
@@ -1,13 +1,14 @@
-<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.0">
+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.1">
     <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
     <macros>
         <import>picard_macros.xml</import>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="3.3.1">r</requirement>
+        <requirement type="package" version="324">ucsc-gff3togenepred</requirement>
+        <requirement type="package" version="324">ucsc-gtftogenepred</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
-
       ## Set up input files
       @symlink_element_identifier@
       ## Reference sequences
@@ -23,7 +24,18 @@
       ## 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"$10}' > refFlat.tab &&
+      #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
+        #if $gene_reference_source.refFlat.ext != 'gff3'
+            gtfToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+        #else
+            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+        #end if
+
+        grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
+      #else
+        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 &&
+      #end if
+
 
       ## Start picard command
 
@@ -33,7 +45,7 @@
       REF_FLAT=refFlat.tab
 
       #if str( $ribosomal_intervals ) != "None":
-	 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
+        RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
       #end if
 
       STRAND_SPECIFICITY="${strand_specificity}"
@@ -41,7 +53,7 @@
       CHART_OUTPUT="${pdfFile}"
 
       #for $sequence_to_ignore in $ignore_list:
-	 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
+        IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
       #end for
 
       RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
@@ -50,9 +62,7 @@
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${reference_fasta_filename}"
       ASSUME_SORTED="${assume_sorted}"
-
-      QUIET=true
-      VERBOSITY=ERROR
+     
       VALIDATION_STRINGENCY=${validation_stringency}
 
    ]]></command>
@@ -60,21 +70,42 @@
    <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" />
       <conditional name="reference_source">
-	 <param name="reference_source_selector" type="select" label="Load reference genome from">
-	    <option value="cached">Local cache</option>
-	    <option value="history">History</option>
-	 </param>
-	 <when value="cached">
-	    <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
-	       <options from_data_table="all_fasta"></options>
-	       <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-	    </param>
-	 </when>
-	 <when value="history">
-	    <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
-	 </when>
+         <param name="reference_source_selector" type="select" label="Load reference genome from">
+            <option value="cached">Local cache</option>
+            <option value="history">History</option>
+         </param>
+         <when value="cached">
+            <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
+               <options from_data_table="all_fasta"></options>
+               <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+            </param>
+         </when>
+         <when value="history">
+            <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
+         </when>
       </conditional>
-      <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" />
+
+      <conditional name="gene_reference_source">
+         <param name="gene_reference_source_selector" type="select" label="Load gene annotation from">
+            <option value="gtf">GTF/GFF3</option>
+            <option value="refflat">refFlat</option>
+         </param>
+         <when value="gtf">
+              <param name="refFlat"
+                     format="gtf,gff3"
+                     type="data"
+                     label="Gene annotation (GTF/GFF3)"/>
+         </when>
+         <when value="refflat">
+              <param name="refFlat"
+                     format="tabular"
+                     type="data"
+                     label="Gene annotations in refFlat form"
+                     help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help"/>
+         </when>
+      </conditional>
+
+
       <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" selected="True">None</option>
@@ -108,6 +139,8 @@
       <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
       <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
       <param name="assume_sorted" value="true" />
+      
+      <param name="gene_reference_source_selector" value="refflat" />
       <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
       <param name="metric_accumulation_level" value="ALL_READS" />
       <param name="minimum_length" value="500" />
@@ -116,6 +149,35 @@
       <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
 
+    <test>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
+      <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
+      <param name="assume_sorted" value="true" />
+      
+      <param name="gene_reference_source_selector" value="gtf" />
+      <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" />
+      <param name="metric_accumulation_level" value="ALL_READS" />
+      <param name="minimum_length" value="500" />
+      <param name="strand_specificity" value="NONE" />
+      <param name="rrna_fragment_percentage" value="0.8" />
+      <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/>
+    </test>
+
+    <test>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
+      <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
+      <param name="assume_sorted" value="true" />
+      
+      <param name="gene_reference_source_selector" value="gtf" />
+      <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />
+      <param name="metric_accumulation_level" value="ALL_READS" />
+      <param name="minimum_length" value="500" />
+      <param name="strand_specificity" value="NONE" />
+      <param name="rrna_fragment_percentage" value="0.8" />
+      <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>
+    </test>
   </tests>
   <help>
 
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_ARRG_test1.bam
Binary file test-data/picard_ARRG_test1.bam has changed
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics.gff3	Thu Dec 08 06:43:38 2016 -0500
@@ -0,0 +1,70 @@
+##gff-version 3
+chrM	hg19_knownGene	gene	236	368	0.000000	-	.	ID=uc004coq.4; 
+chrM	hg19_knownGene	mRNA	236	368	0.000000	-	.	ID=uc004coq.4.m;Parent=uc004coq.4; 
+chrM	hg19_knownGene	exon	236	368	0.000000	-	.	ID=uc004coq.4.e;Parent=uc004coq.4.m; 
+chrM	hg19_knownGene	gene	651	674	0.000000	+	.	ID=uc022bqo.2; 
+chrM	hg19_knownGene	mRNA	651	674	0.000000	+	.	ID=uc022bqo.2.m;Parent=uc022bqo.2; 
+chrM	hg19_knownGene	exon	651	674	0.000000	+	.	ID=uc022bqo.2.e;Parent=uc022bqo.2.m; 
+chrM	hg19_knownGene	gene	1604	1634	0.000000	+	.	ID=uc004cor.1; 
+chrM	hg19_knownGene	mRNA	1604	1634	0.000000	+	.	ID=uc004cor.1.m;Parent=uc004cor.1; 
+chrM	hg19_knownGene	exon	1604	1634	0.000000	+	.	ID=uc004cor.1.e;Parent=uc004cor.1.m; 
+chrM	hg19_knownGene	gene	1844	4264	0.000000	+	.	ID=uc004cos.5; 
+chrM	hg19_knownGene	mRNA	1844	4264	0.000000	+	.	ID=uc004cos.5.m;Parent=uc004cos.5; 
+chrM	hg19_knownGene	exon	1844	4264	0.000000	+	.	ID=uc004cos.5.e;Parent=uc004cos.5.m; 
+chrM	hg19_knownGene	gene	5544	5566	0.000000	-	.	ID=uc022bqp.1; 
+chrM	hg19_knownGene	mRNA	5544	5566	0.000000	-	.	ID=uc022bqp.1.m;Parent=uc022bqp.1; 
+chrM	hg19_knownGene	exon	5544	5566	0.000000	-	.	ID=uc022bqp.1.e;Parent=uc022bqp.1.m; 
+chrM	hg19_knownGene	gene	5586	5606	0.000000	-	.	ID=uc022bqq.1; 
+chrM	hg19_knownGene	mRNA	5586	5606	0.000000	-	.	ID=uc022bqq.1.m;Parent=uc022bqq.1; 
+chrM	hg19_knownGene	exon	5586	5606	0.000000	-	.	ID=uc022bqq.1.e;Parent=uc022bqq.1.m; 
+chrM	hg19_knownGene	gene	5691	5714	0.000000	-	.	ID=uc022bqr.1; 
+chrM	hg19_knownGene	mRNA	5691	5714	0.000000	-	.	ID=uc022bqr.1.m;Parent=uc022bqr.1; 
+chrM	hg19_knownGene	exon	5691	5714	0.000000	-	.	ID=uc022bqr.1.e;Parent=uc022bqr.1.m; 
+chrM	hg19_knownGene	gene	5905	7439	0.000000	+	.	ID=uc031tga.1; 
+chrM	hg19_knownGene	mRNA	5905	7439	0.000000	+	.	ID=uc031tga.1.m;Parent=uc031tga.1; 
+chrM	hg19_knownGene	exon	5905	7439	0.000000	+	.	ID=uc031tga.1.e;Parent=uc031tga.1.m; 
+chrM	hg19_knownGene	gene	7587	7982	0.000000	-	.	ID=uc022bqs.1; 
+chrM	hg19_knownGene	mRNA	7587	7982	0.000000	-	.	ID=uc022bqs.1.m;Parent=uc022bqs.1; 
+chrM	hg19_knownGene	exon	7587	7982	0.000000	-	.	ID=uc022bqs.1.e;Parent=uc022bqs.1.m; 
+chrM	hg19_knownGene	gene	15504	15888	0.000000	-	.	ID=uc022bqs.1; 
+chrM	hg19_knownGene	mRNA	15504	15888	0.000000	-	.	ID=uc022bqs.1.m;Parent=uc022bqs.1; 
+chrM	hg19_knownGene	exon	15504	15888	0.000000	-	.	ID=uc022bqs.1.e;Parent=uc022bqs.1.m; 
+chrM	hg19_knownGene	gene	7587	9208	0.000000	+	.	ID=uc011mfi.2; 
+chrM	hg19_knownGene	mRNA	7587	9208	0.000000	+	.	ID=uc011mfi.2.m;Parent=uc011mfi.2; 
+chrM	hg19_knownGene	exon	7587	9208	0.000000	+	.	ID=uc011mfi.2.e;Parent=uc011mfi.2.m; 
+chrM	hg19_knownGene	gene	8367	8472	0.000000	-	.	ID=uc022bqt.1; 
+chrM	hg19_knownGene	mRNA	8367	8472	0.000000	-	.	ID=uc022bqt.1.m;Parent=uc022bqt.1; 
+chrM	hg19_knownGene	exon	8367	8472	0.000000	-	.	ID=uc022bqt.1.e;Parent=uc022bqt.1.m; 
+chrM	hg19_knownGene	gene	13450	14149	0.000000	-	.	ID=uc022bqt.1; 
+chrM	hg19_knownGene	mRNA	13450	14149	0.000000	-	.	ID=uc022bqt.1.m;Parent=uc022bqt.1; 
+chrM	hg19_knownGene	exon	13450	14149	0.000000	-	.	ID=uc022bqt.1.e;Parent=uc022bqt.1.m; 
+chrM	hg19_knownGene	gene	10060	10404	0.000000	+	.	ID=uc022bqu.2; 
+chrM	hg19_knownGene	mRNA	10060	10404	0.000000	+	.	ID=uc022bqu.2.m;Parent=uc022bqu.2; 
+chrM	hg19_knownGene	exon	10060	10404	0.000000	+	.	ID=uc022bqu.2.e;Parent=uc022bqu.2.m; 
+chrM	hg19_knownGene	gene	10471	12138	0.000000	+	.	ID=uc004cov.5; 
+chrM	hg19_knownGene	mRNA	10471	12138	0.000000	+	.	ID=uc004cov.5.m;Parent=uc004cov.5; 
+chrM	hg19_knownGene	exon	10471	12138	0.000000	+	.	ID=uc004cov.5.e;Parent=uc004cov.5.m; 
+chrM	hg19_knownGene	gene	10761	11231	0.000000	-	.	ID=uc031tgb.1; 
+chrM	hg19_knownGene	mRNA	10761	11231	0.000000	-	.	ID=uc031tgb.1.m;Parent=uc031tgb.1; 
+chrM	hg19_knownGene	exon	10761	11231	0.000000	-	.	ID=uc031tgb.1.e;Parent=uc031tgb.1.m; 
+chrM	hg19_knownGene	gene	13979	14149	0.000000	-	.	ID=uc031tgb.1; 
+chrM	hg19_knownGene	mRNA	13979	14149	0.000000	-	.	ID=uc031tgb.1.m;Parent=uc031tgb.1; 
+chrM	hg19_knownGene	exon	13979	14149	0.000000	-	.	ID=uc031tgb.1.e;Parent=uc031tgb.1.m; 
+chrM	hg19_knownGene	gene	12208	12264	0.000000	+	.	ID=uc004cow.2; 
+chrM	hg19_knownGene	mRNA	12208	12264	0.000000	+	.	ID=uc004cow.2.m;Parent=uc004cow.2; 
+chrM	hg19_knownGene	exon	12208	12264	0.000000	+	.	ID=uc004cow.2.e;Parent=uc004cow.2.m; 
+chrM	hg19_knownGene	gene	12908	14149	0.000000	+	.	ID=uc004cox.4; 
+chrM	hg19_knownGene	mRNA	12908	14149	0.000000	+	.	ID=uc004cox.4.m;Parent=uc004cox.4; 
+chrM	hg19_knownGene	exon	12908	14149	0.000000	+	.	ID=uc004cox.4.e;Parent=uc004cox.4.m; 
+chrM	hg19_knownGene	gene	14675	14698	0.000000	-	.	ID=uc022bqv.1; 
+chrM	hg19_knownGene	mRNA	14675	14698	0.000000	-	.	ID=uc022bqv.1.m;Parent=uc022bqv.1; 
+chrM	hg19_knownGene	exon	14675	14698	0.000000	-	.	ID=uc022bqv.1.e;Parent=uc022bqv.1.m; 
+chrM	hg19_knownGene	gene	14857	15888	0.000000	+	.	ID=uc022bqw.1; 
+chrM	hg19_knownGene	mRNA	14857	15888	0.000000	+	.	ID=uc022bqw.1.m;Parent=uc022bqw.1; 
+chrM	hg19_knownGene	exon	14857	15888	0.000000	+	.	ID=uc022bqw.1.e;Parent=uc022bqw.1.m; 
+chrM	hg19_knownGene	gene	15960	16024	0.000000	-	.	ID=uc022bqx.1; 
+chrM	hg19_knownGene	mRNA	15960	16024	0.000000	-	.	ID=uc022bqx.1.m;Parent=uc022bqx.1; 
+chrM	hg19_knownGene	exon	15960	16024	0.000000	-	.	ID=uc022bqx.1.e;Parent=uc022bqx.1.m; 
+chrM	hg19_knownGene	gene	15999	16571	0.000000	+	.	ID=uc004coz.1; 
+chrM	hg19_knownGene	mRNA	15999	16571	0.000000	+	.	ID=uc004coz.1.m;Parent=uc004coz.1; 
+chrM	hg19_knownGene	exon	15999	16571	0.000000	+	.	ID=uc004coz.1.e;Parent=uc004coz.1.m; 
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics.gtf	Thu Dec 08 06:43:38 2016 -0500
@@ -0,0 +1,23 @@
+chrM	hg19_knownGene	exon	236	368	0.000000	-	.	gene_id "uc004coq.4"; transcript_id "uc004coq.4"; 
+chrM	hg19_knownGene	exon	651	674	0.000000	+	.	gene_id "uc022bqo.2"; transcript_id "uc022bqo.2"; 
+chrM	hg19_knownGene	exon	1604	1634	0.000000	+	.	gene_id "uc004cor.1"; transcript_id "uc004cor.1"; 
+chrM	hg19_knownGene	exon	1844	4264	0.000000	+	.	gene_id "uc004cos.5"; transcript_id "uc004cos.5"; 
+chrM	hg19_knownGene	exon	5544	5566	0.000000	-	.	gene_id "uc022bqp.1"; transcript_id "uc022bqp.1"; 
+chrM	hg19_knownGene	exon	5586	5606	0.000000	-	.	gene_id "uc022bqq.1"; transcript_id "uc022bqq.1"; 
+chrM	hg19_knownGene	exon	5691	5714	0.000000	-	.	gene_id "uc022bqr.1"; transcript_id "uc022bqr.1"; 
+chrM	hg19_knownGene	exon	5905	7439	0.000000	+	.	gene_id "uc031tga.1"; transcript_id "uc031tga.1"; 
+chrM	hg19_knownGene	exon	7587	7982	0.000000	-	.	gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; 
+chrM	hg19_knownGene	exon	15504	15888	0.000000	-	.	gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; 
+chrM	hg19_knownGene	exon	7587	9208	0.000000	+	.	gene_id "uc011mfi.2"; transcript_id "uc011mfi.2"; 
+chrM	hg19_knownGene	exon	8367	8472	0.000000	-	.	gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; 
+chrM	hg19_knownGene	exon	13450	14149	0.000000	-	.	gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; 
+chrM	hg19_knownGene	exon	10060	10404	0.000000	+	.	gene_id "uc022bqu.2"; transcript_id "uc022bqu.2"; 
+chrM	hg19_knownGene	exon	10471	12138	0.000000	+	.	gene_id "uc004cov.5"; transcript_id "uc004cov.5"; 
+chrM	hg19_knownGene	exon	10761	11231	0.000000	-	.	gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; 
+chrM	hg19_knownGene	exon	13979	14149	0.000000	-	.	gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; 
+chrM	hg19_knownGene	exon	12208	12264	0.000000	+	.	gene_id "uc004cow.2"; transcript_id "uc004cow.2"; 
+chrM	hg19_knownGene	exon	12908	14149	0.000000	+	.	gene_id "uc004cox.4"; transcript_id "uc004cox.4"; 
+chrM	hg19_knownGene	exon	14675	14698	0.000000	-	.	gene_id "uc022bqv.1"; transcript_id "uc022bqv.1"; 
+chrM	hg19_knownGene	exon	14857	15888	0.000000	+	.	gene_id "uc022bqw.1"; transcript_id "uc022bqw.1"; 
+chrM	hg19_knownGene	exon	15960	16024	0.000000	-	.	gene_id "uc022bqx.1"; transcript_id "uc022bqx.1"; 
+chrM	hg19_knownGene	exon	15999	16571	0.000000	+	.	gene_id "uc004coz.1"; transcript_id "uc004coz.1"; 
\ No newline at end of file
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test1.tab
--- a/test-data/picard_CollectRnaSeqMetrics_test1.tab	Wed Dec 07 14:56:30 2016 -0500
+++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab	Thu Dec 08 06:43:38 2016 -0500
@@ -1,7 +1,7 @@
 ## htsjdk.samtools.metrics.StringHeader
-# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT    STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_4.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_5.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false 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: Mon Oct 06 22:24:48 EDT 2014
+# Started on: Thu Dec 08 10:54:07 CET 2016
 
 ## METRICS CLASS	picard.analysis.RnaSeqMetrics
 PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test2.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab	Thu Dec 08 06:43:38 2016 -0500
@@ -0,0 +1,10 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_9.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_10.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false 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 Dec 08 10:54:36 CET 2016
+
+## METRICS CLASS	picard.analysis.RnaSeqMetrics
+PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
+48870	48712		0	0	0	48712	0	0	0		0	0	0	1	0	0	0	0	0	0	0			
+
+
diff -r 465cbb0cf2eb -r 00fe2ff64467 test-data/picard_CollectRnaSeqMetrics_test3.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics_test3.tab	Thu Dec 08 06:43:38 2016 -0500
@@ -0,0 +1,113 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa    STOP_AFTER=0 VERBOSITY=INFO QUIET=false 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 Dec 08 10:55:06 CET 2016
+
+## METRICS CLASS	picard.analysis.RnaSeqMetrics
+PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
+48870	48712		0	38786	0	9926	0	0	0		0	0.796231	0	0.203769	0.796231	0.793657	0	0.91593	0.430026	0.235755	1.402829			
+
+## HISTOGRAM	java.lang.Integer
+normalized_position	All_Reads.normalized_coverage
+0	0.313906
+1	0.333933
+2	0.365536
+3	0.344525
+4	0.371353
+5	0.378606
+6	0.518015
+7	0.51266
+8	0.500497
+9	0.690539
+10	0.829611
+11	0.784227
+12	0.825037
+13	0.730533
+14	0.73133
+15	0.693057
+16	0.873759
+17	0.774195
+18	0.721989
+19	0.791727
+20	0.697702
+21	0.698451
+22	0.568885
+23	0.689955
+24	0.580475
+25	0.602348
+26	0.657286
+27	0.600594
+28	0.48185
+29	0.478605
+30	0.646053
+31	0.689366
+32	0.740073
+33	0.695415
+34	0.708419
+35	0.714707
+36	0.707421
+37	0.793703
+38	0.84384
+39	0.819497
+40	0.982412
+41	1.172387
+42	1.28116
+43	1.379184
+44	1.416285
+45	1.32892
+46	1.248258
+47	1.308676
+48	1.085518
+49	1.006687
+50	0.851309
+51	0.693805
+52	0.672921
+53	0.684999
+54	0.62579
+55	0.529832
+56	0.546564
+57	0.566014
+58	0.615824
+59	0.565042
+60	0.547677
+61	0.642067
+62	0.83636
+63	0.937071
+64	1.057465
+65	1.168829
+66	1.375228
+67	1.489487
+68	1.530099
+69	1.287542
+70	1.442585
+71	1.347823
+72	1.424913
+73	1.468345
+74	1.796846
+75	1.79639
+76	1.747908
+77	1.76867
+78	1.773528
+79	1.670178
+80	1.740083
+81	1.809632
+82	2.019967
+83	2.201517
+84	2.150455
+85	2.327367
+86	2.261259
+87	1.929731
+88	1.936627
+89	1.80697
+90	1.789004
+91	1.642341
+92	1.408203
+93	1.159737
+94	0.990047
+95	0.697842
+96	0.377809
+97	0.243433
+98	0.218816
+99	0.223665
+100	0.225079
+