# HG changeset patch
# User devteam
# Date 1393480995 18000
# Node ID 08b3cb5ce6517f8d7bf3a95200232271142b55d9
# Parent  5844a1604c0c91cf8c6912e0201bdc1806bb5c47
Uploaded

diff -r 5844a1604c0c -r 08b3cb5ce651 picard_CollectRnaSeqMetrics.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectRnaSeqMetrics.xml	Thu Feb 27 01:03:15 2014 -0500
@@ -0,0 +1,103 @@
+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.106.0">
+<description>Collect RNA-Seq Metrics</description>
+<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
+   <command interpreter="python">
+      picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
+    -n "${out_prefix}" --tmpdir "${__new_file_path__}" --assumesorted ${ASSUME_SORTED}
+    --refflat ${REF_FLAT}
+    #if $identify_ribosomal.opt == "yes"
+    	--ribosomalintervals ${identify_ribosomal.RIBOSOMAL_INTERVALS}
+    #end if
+    --malevel "${malevel}"
+    --minlength ${MINIMUM_LENGTH}
+    --strandspecificity ${STRAND_SPECIFICITY}
+    --rrnafragmentpercentage ${RRNA_FRAGMENT_PERCENTAGE}
+    #for $i in $IGNORE_SEQUENCES
+        --ignoreseq "${i.IGNORE_SEQUENCE}"
+    #end for 
+    -j "\$JAVA_JAR_PATH/CollectRnaSeqMetrics.jar"
+  </command>
+    
+  <stdio>
+    <exit_code range="0" level="warning" description="Tool finished correctly" />
+  </stdio>
+   
+  <inputs>
+  	<param format="sam" name="input_file" type="data" label="Input SAM file." help="" />
+        <param name="out_prefix" value="RNA-Seq Metrics" type="text"
+      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
+
+      <param format="data" name="REF_FLAT" type="data" label="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required." help="" />
+      
+    <conditional name="identify_ribosomal">
+      <param name="opt" type="select" label="Identify ribosomal bases" help="If 'no' is selected, no bases will be identified as being ribosomal.">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="no" />
+      <when value="yes">
+        <param format="data" name="RIBOSOMAL_INTERVALS" type="data" label="Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html Default value: null." help="" />
+       </when>
+    </conditional>      
+      
+      <param name="STRAND_SPECIFICITY" type="select" label="For strand-specific library prep." help="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>
+            <option value="FIRST_READ_TRANSCRIPTION_STRAND">FIRST_READ_TRANSCRIPTION_STRAND</option>
+            <option value="SECOND_READ_TRANSCRIPTION_STRAND">SECOND_READ_TRANSCRIPTION_STRAND</option>
+      </param>
+      
+      <param name="MINIMUM_LENGTH" type="text" value="500" label="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater." help="" />
+      
+     <repeat name="IGNORE_SEQUENCES" title="Ignore Sequences">
+      <param name="IGNORE_SEQUENCE" label="Ignore Sequence" type="text" help="If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases." />
+    </repeat>
+      
+      <param name="RRNA_FRAGMENT_PERCENTAGE" type="text" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair by this must in order to be considered rRNA." help="" />
+      
+      <param name="malevel" value="0" type="select" multiple="true"  label="Metric Accumulation Level"
+      help="Level(s) at which metrics will be accumulated">
+      <option value="ALL_READS" selected="true">All reads (default)</option>
+      <option value="SAMPLE" default="true">Sample</option>
+      <option value="LIBRARY" default="true">Library</option>
+      <option value="READ_GROUP" default="true">Read group</option>
+     </param>      
+      
+      <param  checked="True" truevalue="true" falsevalue="false" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored." />
+  </inputs>
+  <outputs>
+    		<data format="html" name="html_file"  label="${out_prefix}.html"/>
+  </outputs>
+  <tests>
+    <test>
+       <!-- python picard_wrapper.py 
+            -i "/home/~/PICARD-in.sam" 
+            -d "/home/~/outputrnaseqùetrics_files" 
+            -t "/home/~/outputrnaseqmetrics.htm"     
+            -n "RNA-Seq Metrics" 
+            --tmpdir "/home/dorine/galaxypicard/galaxy-central/database/tmp" 
+            --assumesorted true     
+            --refflat /home/~/refFlat.txt     --malevel "ALL_READS"     --minlength 500     --strandspecificity NONE     
+            --rrnafragmentpercentage 0.8     -j "/home/~/CollectRnaSeqMetrics.jar" -->
+       <param name="inputFile" value="PICARD-in.sam" />
+       <param name="out_prefix" value="RNA-Seq Metrics" />
+       <param name="ASSUME_SORTED" value="true" />
+       <param name="REF_FLAT" value="refFlat.txt" />
+       <param name="malevel" value="ALL_READS" />
+       <param name="MINIMUM_LENGTH" value="500" />
+       <param name="STRAND_SPECIFICITY" value="NONE" />
+       <param name="RRNA_FRAGMENT_PERCENTAGE" value="O.8" />
+       <output name="html_file" file="outputrnaseqmetrics.html" ftype="html" lines_diff="30"/>
+    </test>
+  </tests>
+  <help>
+Picard documentation says:
+ 
+  
+CollectRnaSeqMetrics
+
+Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CollectRnaSeqMetrics
+
+Program to collect metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal. Also determines strand-specificity for strand-specific libraries.
+
+  </help>
+</tool>