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changeset 138:987dbea3b72f draft

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Uploaded
author devteam
date Thu, 27 Feb 2014 01:00:20 -0500
parents 90e36e359db6
children 5844a1604c0c
files test-data/outputrnaseqmetrics.html
diffstat 1 files changed, 59 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputrnaseqmetrics.html	Thu Feb 27 01:00:20 2014 -0500
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+<style type="text/css">
+tr.d0 td {background-color: oldlace; color: black;}
+tr.d1 td {background-color: aliceblue; color: black;}
+</style><?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
+<title></title>
+<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
+</head>
+<body>
+<div class="document">
+Galaxy tool CollectRnaSeqMetrics run at 26/02/2014 22:17:36</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
+<tr><td><a href="CollectRnaSeqMetrics.log">CollectRnaSeqMetrics.log</a></td></tr>
+<tr><td><a href="CollectRnaSeqMetrics.metrics.txt">CollectRnaSeqMetrics.metrics.txt</a></td></tr>
+</table><p/>
+<b>Picard on line resources</b><ul>
+<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
+<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
+<b>Picard output (transposed to make it easier to see)</b><hr/>
+<table cellpadding="3" >
+<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt RIBOSOMAL_INTERVALS=null STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=CollectRnaSeqMetrics.pdf RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam OUTPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Wed Feb 26 22:17:31 EST 2014</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.analysis.RnaSeqMetrics</td></tr><tr class="d0"><td>PF_BASES</td><td>7321300&nbsp;</td></tr>
+<tr class="d1"><td>PF_ALIGNED_BASES</td><td>7319805&nbsp;</td></tr>
+<tr class="d0"><td>RIBOSOMAL_BASES</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>CODING_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>UTR_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>INTRONIC_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>INTERGENIC_BASES</td><td>7319805&nbsp;</td></tr>
+<tr class="d1"><td>IGNORED_READS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>CORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>INCORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_RIBOSOMAL_BASES</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>PCT_CODING_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_UTR_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PCT_INTRONIC_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_INTERGENIC_BASES</td><td>1&nbsp;</td></tr>
+<tr class="d1"><td>PCT_MRNA_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>PCT_USABLE_BASES</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>PCT_CORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>MEDIAN_CV_COVERAGE</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>MEDIAN_5PRIME_BIAS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>MEDIAN_3PRIME_BIAS</td><td>0&nbsp;</td></tr>
+<tr class="d1"><td>MEDIAN_5PRIME_TO_3PRIME_BIAS</td><td>0&nbsp;</td></tr>
+<tr class="d0"><td>SAMPLE</td><td>&nbsp;</td></tr>
+<tr class="d1"><td>LIBRARY</td><td>&nbsp;</td></tr>
+<tr class="d0"><td>READ_GROUP
+</td><td>
+&nbsp;</td></tr>
+</table>
+<b>Picard Tool Run Log</b><hr/>
+<pre>INFO:root:## executing java -Xmx3000m  -Djava.io.tmpdir='/home/dorine/galaxypicard/galaxy-central/database/tmp'  -jar /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/CollectRnaSeqMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam O=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt CHART_OUTPUT=CollectRnaSeqMetrics.pdf ASSUME_SORTED=true MINIMUM_LENGTH=500 REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt STRAND_SPECIFICITY=NONE RIBOSOMAL_INTERVALS=null RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=ALL_READS returned status 0 and nothing on stderr
+
+INFO:root:Unable to find expected pdf file /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.pdf<br/>
+
+</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
+generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
+