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summaryReport.xsl
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<?xml version="1.0"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="html" doctype-system="http://www.w3.org/TR/html4/strict.dtd" doctype-public="-//W3C//DTD HTML 4.01//EN" indent="yes" />
<xsl:template name="RepeatString">
<xsl:param name="string" select="''" />
<xsl:param name="times" select="1" />
<xsl:if test="number($times) > 0">
<xsl:value-of select="$string" />
<xsl:call-template name="RepeatString">
<xsl:with-param name="string" select="$string" />
<xsl:with-param name="times" select="$times - 1" />
</xsl:call-template>
</xsl:if>
</xsl:template>
<xsl:template name="format-suffix">
<xsl:param name="myval" />
<xsl:param name="precision" />
<xsl:variable name="zeroes">
<xsl:call-template name="RepeatString">
<xsl:with-param name="string" select="0" />
<xsl:with-param name="times" select="$precision" />
</xsl:call-template>
</xsl:variable>
<xsl:variable name="dval" select="concat(1,$zeroes)" />
<xsl:choose>
<xsl:when test="$myval > 1000000000">
<xsl:value-of select="format-number(round($myval div (1000000000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>G</xsl:text>
</xsl:when>
<xsl:when test="$myval > 1000000">
<xsl:value-of select="format-number(round($myval div (1000000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>M</xsl:text>
</xsl:when>
<xsl:when test="$myval > 1000">
<xsl:value-of select="format-number(round($myval div (1000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>k</xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$myval" />
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="/SummaryReport">
<html>
<head>
<title><xsl:value-of select="MetaData/@RunFolder"/></title>
<style type="text/css">
body {font:12px arial,sans-serif; background:#ffffff}
h1 {text-align: left; padding: 5px; font-weight:bold; font-size:150%;}
h2 {text-align: left; padding: 5px; font-weight:bold; font-size:120%;}
hr {color:sienna;}
p {margin-left:20px; width: 80em;}
tr.even { background: #bbbbbb; }
tr.odd { background: #dddddd; }
thead { background: #eeeeee; }
div.section {display: inline-block; background: #eeeeee; margin-bottom: 20px; margin-right: 20px;}
table th { padding: 1px 10px;}
table td { padding: 1px 10px;}
table td { text-align: center;}
table tr.SampleName { background: #aaaaaa; }
table td.SampleName { text-align: left; padding:10px 5px 5px 5px; font-weight:bold; font-size:125%;}
span.stddev {font-size:75%;}
table.MetaData th { text-align: left; padding: 5px; font-weight:bold; font-size:100%;}
table.MetaData td { text-align: left; padding: 5px; font-size:75%; background:#dddddd}
table.key th { text-align: left; padding: 5px; font-size:75%;}
table.key td { text-align: left; padding: 5px; font-size:75%; background:#dddddd}
</style>
</head>
<body>
<h1>Summary of sequencing results for <xsl:value-of select="MetaData/@RunFolder"/></h1>
<br />
<div>
<div class="section">
<h2>Metrics aggregated per lane</h2>
<table>
<thead>
<tr>
<th>Lane</th>
<th>Raw Density<br/>clusters/mm<sup>2</sup></th>
<th>Excluded<br /> Tiles</th>
<th>Pass<br/>Filter(%)</th>
<th>Clusters<br/>PF</th>
<th>Read</th>
<th>Yield<br/>PF (bp)</th>
<th>Q≥30(%)</th>
<th>Yield<br/>Q≥30 (bp)</th>
<th>MeanQ</th>
<th>Q-score per base<br />A/C/G/T</th>
<th>PhiX<br/>Error<br />(Excluded)</th>
<th>Q-score<br/>distribution</th>
<th>Base<br/>composition</th>
<th>GC<br/>distribution</th>
<th>Contiguous Length<br/>with Q≥30 (bp)</th>
<th>Duplicates</th>
<th>Adapter<br/>sequences</th>
<th>Q-score per base<br/>and position</th>
</tr>
</thead>
<tbody>
<xsl:for-each select="LaneMetrics/Lane">
<xsl:variable name="row-class">
<xsl:choose>
<xsl:when test="position() mod 2 = 0">even</xsl:when>
<xsl:otherwise>odd</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<xsl:variable name="LaneRows">
<xsl:value-of select="count(descendant::Read)"/>
</xsl:variable>
<xsl:for-each select="./Read">
<tr class="{$row-class}">
<xsl:if test="count(preceding-sibling::Read) = 0">
<td rowspan="{$LaneRows}"><xsl:value-of select="../@Id"/></td>
<td rowspan="{$LaneRows}">
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@DensityRaw" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td rowspan="{$LaneRows}">
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@ExcludedTiles" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td rowspan="{$LaneRows}"><xsl:value-of select="@PctPF"/></td>
<td rowspan="{$LaneRows}">
<xsl:attribute name="style">
<xsl:choose>
<xsl:when test="@PF < 140000000">
<xsl:text>background: #ff7777; color: black;</xsl:text>
</xsl:when>
</xsl:choose>
</xsl:attribute>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@PF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
</xsl:if>
<td><xsl:value-of select="@Id"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldPF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<!-- <td><xsl:value-of select="@Q30Fraction"/></td>-->
<td><xsl:value-of select="format-number(round((@YieldQ30 * 1000) div @YieldPF) div 10, '##.0')"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldQ30" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="@QMean"/><span class="stddev">±<xsl:value-of select="@QStdDev"/></span></td>
<td>
<xsl:value-of select="@QValuePerBaseAMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseAStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseCMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseCStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseGMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseGStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseTMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseTStdv"/></span>
</td>
<td>
<xsl:attribute name="style">
<xsl:choose>
<xsl:when test="@ErrRate > 2">
<xsl:text>background: #ff7777; color: black;</xsl:text>
</xsl:when>
</xsl:choose>
</xsl:attribute>
<xsl:value-of select="@ErrRate"/>
<span class="stddev">±<xsl:value-of select="@ErrRateSD"/></span>
<xsl:if test="@ExcludedTiles > 0">
<br />(
<xsl:value-of select="Excluded/@ErrRate"/>
<span class="stddev">±<xsl:value-of select="Excluded/@ErrRateSD"/></span>
)
</xsl:if>
</td>
<xsl:choose>
<xsl:when test="@QscorePlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QscorePlot)}"><img alt="Qscore Plot" src="{concat('./',@QscorePlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@BaseCompPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@BaseCompPlot)}"><img alt="Base Composition Plot" src="{concat('./',@BaseCompPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@GCPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@GCPlot)}"><img alt="GC Plot" src="{concat('./',@GCPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@Q30Plot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@Q30Plot)}"><img alt="Q30Length Plot" src="{concat('./',@Q30PlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@DupPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@DupPlot)}"><img alt="Duplication Plot" src="{concat('./',@DupPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@AdapterPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@AdapterPlot)}"><img alt="Adapter Plot" src="{concat('./',@AdapterPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@QValuePerBase = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QValuePerBase)}"><img alt="Q-value per base" src="{concat('./',@QValuePerBaseThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
</tr>
</xsl:for-each>
</xsl:for-each>
</tbody>
</table>
</div>
</div>
<div>
<div class="section">
<h2>Metrics aggregated per project</h2>
<table>
<thead>
<tr>
<th>Read</th>
<th>Lane</th>
<th>Yield<br/>PF (bp)</th>
<th>Clusters<br/>PF</th>
<th>Q≥30(%)</th>
<th>Yield<br/>Q≥30 (bp)</th>
<th>MeanQ</th>
<th>Q-score per base<br />A/C/G/T</th>
<th>Q-score<br/>distribution</th>
<th>Base<br/>composition</th>
<th>GC<br/>distribution</th>
<th>Contiguous Length<br/>with Q≥30 (bp)</th>
<th>Duplicates</th>
<th>Adapter<br/>sequences</th>
<th>Q-score per base<br/> and position</th>
</tr>
</thead>
<tbody>
<xsl:for-each select="ProjectMetrics/Project">
<tr class="SampleName">
<td colspan="15" class="SampleName"><a href="{concat('./', @Id, '/report.html')}"><xsl:value-of select="@Id"/></a></td>
</tr>
<xsl:for-each select="./Read">
<xsl:variable name="row-class">
<xsl:choose>
<xsl:when test="position() mod 2 = 0">even</xsl:when>
<xsl:otherwise>odd</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<xsl:variable name="LaneRows">
<xsl:value-of select="count(descendant::Lane)"/>
</xsl:variable>
<xsl:for-each select="./Lane">
<tr class="{$row-class}">
<xsl:attribute name="style">
<xsl:choose>
<!-- Set red background if Undetermined sequences has more data than half of that expected per sample -->
<xsl:when test="../../@Id='Undetermined_indices' and @PctLane > (50 div /SummaryReport/LaneMetrics/Lane[@Id=current()/@Id]/Read[@Id=1]/@SamplesOnLane)">
<xsl:text>background: #ff7777; color: black;</xsl:text>
</xsl:when>
</xsl:choose>
</xsl:attribute>
<xsl:if test="count(preceding-sibling::Lane) = 0">
<td rowspan="{$LaneRows}"><xsl:value-of select="../@Id"/></td>
</xsl:if>
<td><xsl:value-of select="@Id"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldPF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@PF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="format-number(round((@YieldQ30 * 1000) div @YieldPF) div 10, '##.0')"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldQ30" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="@QMean"/><span class="stddev">±<xsl:value-of select="@QStdDev"/></span></td>
<td>
<xsl:value-of select="@QValuePerBaseAMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseAStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseCMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseCStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseGMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseGStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseTMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseTStdv"/></span>
</td>
<xsl:choose>
<xsl:when test="@QscorePlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QscorePlot)}"><img alt="Qscore Plot" src="{concat('./',@QscorePlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@BaseCompPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@BaseCompPlot)}"><img alt="Base Composition Plot" src="{concat('./',@BaseCompPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@GCPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@GCPlot)}"><img alt="GC Plot" src="{concat('./',@GCPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@Q30Plot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@Q30Plot)}"><img alt="Q30Length Plot" src="{concat('./',@Q30PlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@DupPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@DupPlot)}"><img alt="Duplication Plot" src="{concat('./',@DupPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@AdapterPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@AdapterPlot)}"><img alt="Adapter Plot" src="{concat('./',@AdapterPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@QValuePerBase = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QValuePerBase)}"><img alt="Q-value per base" src="{concat('./',@QValuePerBaseThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
</tr>
</xsl:for-each>
</xsl:for-each>
</xsl:for-each>
</tbody>
</table>
</div>
</div>
<div>
<div class="section">
<h2>Run parameters</h2>
<table class="MetaData">
<tr class="odd">
<td>Run Folder</td>
<td><xsl:value-of select="MetaData/@RunFolder"/></td>
</tr>
<xsl:for-each select="MetaData/Read">
<tr >
<td>Read <xsl:value-of select="@Id"/></td>
<td><xsl:value-of select="@Cycles"/>bp</td>
</tr>
</xsl:for-each>
<tr >
<td>Cluster Kit</td>
<td><xsl:value-of select="MetaData/@ClusterKitVersion"/></td>
</tr>
<tr >
<td>Flow Cell ID</td>
<td><xsl:value-of select="MetaData/@FlowCellId"/></td>
</tr>
<tr >
<td>Flow Cell Version</td>
<td><xsl:value-of select="MetaData/@FlowCellVer"/></td>
</tr>
<tr >
<td>Chemistry</td>
<td><xsl:value-of select="MetaData/@SBSversion"/></td>
</tr>
<tr >
<td>Instrument Type</td>
<td><xsl:value-of select="MetaData/@InstrumentModel"/></td>
</tr>
<tr >
<td>HiSeq Control Software</td>
<td><xsl:value-of select="MetaData/@CsVersion"/></td>
</tr>
<tr >
<td>RTA Version</td>
<td><xsl:value-of select="MetaData/@RtaVersion"/></td>
</tr>
<tr >
<td>Sisyphus Version</td>
<td><xsl:value-of select="MetaData/@SisyphusVersion"/></td>
</tr>
<tr >
<td>Q-Score Offset</td>
<td><xsl:value-of select="MetaData/@Qoffset"/></td>
</tr>
</table>
</div>
<div class="section">
<h2>Table key</h2>
<table class="key">
<tr>
<td>Raw Density</td>
<td>Average number of clusters per square mm</td>
</tr>
<tr>
<td>Pass Filter</td>
<td>Fraction of sequences that passed Illumina's chastity filter. Only the sequences that passed the filter are reported</td>
</tr>
<tr>
<td>Yield PF</td>
<td>Total number of bases from pass filter reads</td>
</tr>
<tr>
<td>Clusters PF</td>
<td>Number of clusters (sequences) pass filter</td>
</tr>
<tr>
<td>Q≥30</td>
<td>Fraction of all pass filter bases with Q-score ≥30</td>
</tr>
<tr>
<td>Yield Q≥30</td>
<td>Number of bases with Q-score ≥30</td>
</tr>
<tr>
<td>MeanQ</td>
<td>Mean Q-score over all sequences (±Standard deviation)</td>
</tr>
<tr>
<td>Q-score distribution</td>
<td>A plot showing the distribution of Q-scores per cycle</td>
</tr>
<tr>
<td>Base composition</td>
<td>Plot on the relative fraction of each base per cycle</td>
</tr>
<tr>
<td>GC distribution</td>
<td>Distribution of GC-content in the sequenced fragments</td>
</tr>
<tr>
<td>Contiguous Length with Q≥30</td>
<td>Plot on the length distribution of the longest contiguous stretch of bases with Q-score < 30</td>
</tr>
<tr>
<td>Duplicates</td>
<td>Frequency of duplicated sequences. The numbers are estimated by following the first 100,000 unique sequences through the whole file.
Identity is based on the first 50 bases.</td>
</tr>
<tr>
<td>Adapter sequences</td>
<td>Cumulative fraction of sequences matching the adapter sequence, starting at cycle X. The match must be at least 6 bases, have at most 1 mismatch per 10 bases and extend to the end of the read or adapter sequence.</td>
</tr>
</table>
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