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biopet.biopet
Commit 38e13cdd authored by Peter van 't Hof's avatar Peter van 't Hof
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Switch to krona plots

parent dceac7c8
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Showing with 62 additions and 5 deletions
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/krona.ssp 0 → 100644
View file @ 38e13cdd
#import(java.io.File)
#import(scala.io.Source)
<%@ var rootPath: String %>
<%@ var kronaXml: File %>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta charset="utf-8"/>
<link rel="shortcut icon" href="${rootPath}ext/img/krona/favicon.ico"/>
<!--<script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>-->
<script src="${rootPath}ext/js/krona-2.0.js"></script>
</head>
<body>
<img id="hiddenImage" src="${rootPath}ext/img/krona/hidden.png" style="display:none"/>
<img id="loadingImage" src="${rootPath}ext/img/krona/loading.gif" style="display:none"/>
<noscript>Javascript must be enabled to view this page.</noscript>
<div style="display:none">
<%
val reader = Source.fromFile(kronaXml)
val xml = reader.getLines().mkString("\n")
reader.close()
%>
${unescape(xml)}
</div></body></html>
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @ 38e13cdd
......@@ -148,7 +148,7 @@
${name}
</h3>
</div>
${unescape(section.render(args))}
${unescape(section.render(args ++ Map("args" -> args)))}
</div>
#end
</div>
......
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp 0 → 100644
View file @ 38e13cdd
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.core.report.ReportBuilder)
#import(nl.lumc.sasc.biopet.pipelines.gears.GearsKraken)
#import(java.io.File)
#import(java.io.PrintWriter)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
<%
val bla = if (sampleId.isEmpty && libId.isEmpty) {
summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
} else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
GearsKraken.convertKrakenSummariesToKronaXml(bla, tempFile)
val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/krona.ssp",
args ++ Map("kronaXml" -> tempFile))
val file = new File(outputDir, "kraken_krona.html")
val writer = new PrintWriter(file)
writer.println(output)
writer.close()
%>
<iframe src="kraken_krona.html" style="width:100%;height:80vh;border:none;"></iframe>
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ 38e13cdd
......@@ -16,7 +16,7 @@ object GearsReport extends MultisampleReportBuilder {
def reportName = "Gears Report"
override def extFiles = super.extFiles ++ List("js/gears.js")
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
......@@ -54,7 +54,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil, List(
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
......
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @ 38e13cdd
......@@ -27,7 +27,7 @@ object GearsSingleReport extends ReportBuilder {
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
override def extFiles = super.extFiles ++ List("js/gears.js")
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
def indexPage = {
......@@ -39,7 +39,7 @@ object GearsSingleReport extends ReportBuilder {
),
List(
"Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp")
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")
),
pageArgs
)
......
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