Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
38e13cdd
Commit
38e13cdd
authored
Dec 24, 2015
by
Peter van 't Hof
Browse files
Switch to krona plots
parent
dceac7c8
Changes
5
Hide whitespace changes
Inline
Side-by-side
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
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment