diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp new file mode 100644 index 0000000000000000000000000000000000000000..39166ca0d29e0d4cf1e8530dd8ca94525f65a659 --- /dev/null +++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp @@ -0,0 +1,24 @@ +#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>