Added testing for qiime biom to krona method

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala

@@ -79,8 +79,6 @@ object GearsQiimeClosed {
       val counts: mutable.Map[String, Long] = mutable.Map()
       def totalCount(sample: String): Long = counts.getOrElse(sample, 0L) + childs.map(_.totalCount(sample)).sum
 
-      override def toString() = s"$level:$name:$counts"
-
       def node: Elem = {
         val sizes = sortedSamples.map { sample => <val>{ totalCount(sample) }</val> }
         val size = <size>{ sizes }</size>

public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosedTest.scala

+package nl.lumc.sasc.biopet.pipelines.gears
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvan_thof on 2/5/16.
+  */
+class GearsQiimeClosedTest extends  TestNGSuite with Matchers {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testQiimeBiomToKrona: Unit = {
+    val qiimeBiomFile = new File(resourcePath("/otu_table.biom"))
+    val outputFile = File.createTempFile("krona.", ".xml")
+    outputFile.deleteOnExit()
+    GearsQiimeClosed.qiimeBiomToKrona(qiimeBiomFile, outputFile)
+  }
+}