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biopet.biopet
Commit 3965ec63 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix tables hide

parent 93c98188
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Showing with 209 additions and 211 deletions
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ 3965ec63
......@@ -27,55 +27,53 @@
</div>
<div class="panel-footer">
#if (showTable)
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#alignmentSummaryTable">Hide table</button>
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#alignmentSummaryTable">Show table</button>
#end
<i class="glyphicon glyphicon-file"></i> <a href="alignmentSummary.tsv">tsv file</a>
</div>
#end
#if (showTable)
<div class="panel-body collapse" id="alignmentSummaryTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
<th>Total</th>
<th>Mapped</th>
<th>(%)</th>
<th>Duplicates</th>
<th>(%)</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
<td>${mapped.toDouble / total * 100}%</td>
<td>${duplicates}</td>
<td>${duplicates.toDouble / total * 100}%</td>
</tr>
#end
<div class="panel-body collapse #if (showTable)in#end" id="alignmentSummaryTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
<th>Total</th>
<th>Mapped</th>
<th>(%)</th>
<th>Duplicates</th>
<th>(%)</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
<td>${mapped.toDouble / total * 100}%</td>
<td>${duplicates}</td>
<td>${duplicates.toDouble / total * 100}%</td>
</tr>
#end
</tbody>
</table>
</div>
#end
</tbody>
</table>
#end
\ No newline at end of file
</div>
\ No newline at end of file
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @ 3965ec63
......@@ -30,52 +30,51 @@
</div>
<div class="panel-footer">
#if (showTable)
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">Hide table</button>
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">Show table</button>
#end
<i class="glyphicon glyphicon-file"></i> <a href="insertsize.tsv">tsv file</a>
</div>
#end
#if (showTable)
<div class="panel-body collapse" id="insertsizeTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List(metricsTag, "stats", "insert_size_metrics", field)):_*)
}
}#
#for (value <- fieldValues)
<td>${value}</td>
#end
</tr>
#end
#end
</tbody>
</table>
</div>
<div class="panel-body collapse #if (showTable)in#end" id="insertsizeTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
#end
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List(metricsTag, "stats", "insert_size_metrics", field)):_*)
}
}#
#for (value <- fieldValues)
<td>${value}</td>
#end
</tr>
#end
#end
</tbody>
</table>
</div>
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @ 3965ec63
......@@ -33,62 +33,63 @@
</div>
<div class="panel-footer">
#if (showTable)
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_BasesTable">Hide table</button>
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_BasesTable">Show table</button>
#end
<i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_R1.tsv">R1 reads stats</a> -
<i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_R2.tsv">R2 reads stats</a>
</div>
#end
#if (showTable)
<div class="panel-body collapse" id="QC_BasesTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<div class="panel-body collapse #if (showTable)in#end" id="QC_BasesTable">
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Discarded</th>
<th>(%)</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).asInstanceOf[Long]
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
}#
<td>${read}</td>
<td>${beforeTotal}</td>
<td>${beforeTotal - afterTotal}</td>
<td>${(beforeTotal - afterTotal).toDouble / beforeTotal * 100}%</td>
<td>${afterTotal}</td>
#end
</tr>
#end
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Discarded</th>
<th>(%)</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).asInstanceOf[Long]
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
}#
<td>${read}</td>
<td>${beforeTotal}</td>
<td>${beforeTotal - afterTotal}</td>
<td>${(beforeTotal - afterTotal).toDouble / beforeTotal * 100}%</td>
<td>${afterTotal}</td>
#end
</tr>
#end
</tbody>
</table>
#end
</tbody>
</table>
</div>
#end
\ No newline at end of file
</div>
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @ 3965ec63
......@@ -34,64 +34,64 @@
</div>
<div class="panel-footer">
#if (showTable)
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Hide table</button>
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Show table</button>
#end
<i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R1.tsv">R1 reads stats</a> -
<i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R2.tsv">R2 reads stats</a>
</div>
#end
#if (showTable)
<div class="panel-body collapse" id="QC_ReadsTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Clipping</th>
<th>Trimming</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).asInstanceOf[Long]
val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).asInstanceOf[Long]
val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).asInstanceOf[Long]
}#
<td>${read}</td>
<td>${beforeTotal}</td>
<td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
<td>${trimmingDiscarded}</td>
<td>${afterTotal}</td>
#end
</tr>
#end
#end
</tbody>
<div class="panel-body collapse #if (showTable)in#end" id="QC_ReadsTable">
</table>
</div>
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Clipping</th>
<th>Trimming</th>
<th>After QC</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).asInstanceOf[Long]
val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).asInstanceOf[Long]
val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).asInstanceOf[Long]
}#
<td>${read}</td>
<td>${beforeTotal}</td>
<td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
<td>${trimmingDiscarded}</td>
<td>${afterTotal}</td>
#end
</tr>
#end
#end
</tbody>
#end
\ No newline at end of file
</table>
</div>
public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
View file @ 3965ec63
......@@ -9,7 +9,7 @@
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
#{
val fields = List("Hom", "HomVar", "HomRef", "NoCall", "Variant", "NonInformative", "Total")
val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
......@@ -23,29 +23,29 @@
</div>
<div class="panel-footer">
#if (showTable)
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#variantSummaryTable">Hide table</button>
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#variantSummaryTable">Show table</button>
#end
<i class="glyphicon glyphicon-file"></i> <a href="variantSummary.tsv">tsv file</a>
</div>
#end
#if (showTable)
<div class="panel-body collapse" id="variantSummaryTable">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#for (field <- fields) <th>${field}</th> #end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (field <- fields)
<td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
#end
</tr>
#end
</tbody>
</table>
</div>
<div class="panel-body collapse #if (showTable)in#end" id="variantSummaryTable">
#end
\ No newline at end of file
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#for (field <- fields) <th>${field}</th> #end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (field <- fields)
<td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
#end
</tr>
#end
</tbody>
</table>
</div>
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @ 3965ec63
......@@ -30,16 +30,16 @@ object ShivaReport extends MultisampleReportBuilder {
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
"Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
Map("showPlot" -> true, "showTable" -> true)),
Map("showPlot" -> true, "showTable" -> false)),
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> true)
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> true)),
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> true)),
Map("showPlot" -> true, "showTable" -> false)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> true))
Map("showPlot" -> true, "showTable" -> false))
),
pageArgs
)
......
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