Commit c8012021 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added template for biom to krona

parent e133158f
#import(nl.lumc.sasc.biopet.core.report.ReportBuilder)
#import(nl.lumc.sasc.biopet.pipelines.gears.GearsQiimeClosed)
#import(java.io.File)
#import(java.io.PrintWriter)
<%@ var biomFile: File %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
<%
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
GearsQiimeClosed.qiimeBiomToKrona(biomFile, 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>
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