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biopet.biopet
Commits
b118cadf
Commit
b118cadf
authored
Mar 20, 2017
by
Peter van 't Hof
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Fixed rna template
parent
a5333b95
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23 additions
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26 deletions
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-26
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
+23
-26
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bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
View file @
b118cadf
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
...
...
@@ -14,13 +17,9 @@
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
...
...
@@ -36,7 +35,7 @@
#end
#if (showPlot)
#{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, lib
rary
Id = libId) }#
<div class="panel-body">
<img src="rna.png" class="img-responsive" />
...
...
@@ -47,7 +46,7 @@
#else
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Show table</button>
#end
<a href="rna.tsv"><button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"></i>
TSV file</button></a>
<a href="rna.tsv"><button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"></i>TSV file</button></a>
</div>
#end
...
...
@@ -62,27 +61,25 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(
""
)
case (Some(
libId), _) => List(libId.toString
)
case _ =>
summary.libraries(sample
).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(
None
)
case (Some(
_), _) => List(libId
)
case _ =>
Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
}/Libraries/${libId}/index.html">${libId
}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample
.name}/Libraries/${libName}/index.html">${libName
}</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("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
}
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (
value <- fieldValue
s)
<td>${
value
}</td>
#for (
field <- field
s)
<td>${
results(field)
}</td>
#end
</tr>
#end
...
...
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