outputBamfiles.ssp 1.79 KB
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#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var sampleLevel: Boolean = true %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
#{
    val samples = sampleId match {
    case Some(sample) => {
    List(sample.toString)
    }
    case _ => summary.samples.toList
    }
}#

<div class="panel-body">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
    <thead><tr>
        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
        #if (!sampleLevel) <th>Library</th> #end
        <th>Path</th>
        <th>MD5</th>
    </tr></thead>
    <tbody>
        #for (sample <- samples.toList.sorted)
            #{
                val libs = (libId, sampleLevel) match {
                case (_, true) => List("")
                case (Some(libId), _) => List(libId.toString)
                case _ => summary.libraries(sample).toList
                }
            }#
            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
            #for (libId <- libs)
                #if (libs.head != libId) <tr> #end
                    #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
                    <td>${summary.getLibraryValue(sample, libId, "shiva", "files", "pipeline", "preProcessBam", "path")}</td>
                    <td>${summary.getLibraryValue(sample, libId, "shiva", "files", "pipeline", "preProcessBam", "md5")}</td>
                </tr>
            #end
        #end
    </tbody>
</table>

</div>