From 2a789532926c87c80925a2e8cc9781632ccc907c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 8 Nov 2014 18:52:17 +0100
Subject: [PATCH] Added Queue wrapper
---
.../lumc/sasc/biopet/tools/MergeAlleles.scala | 22 ++++++++++++++++++-
1 file changed, 21 insertions(+), 1 deletion(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 781749456..1ccaf687b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -9,11 +9,31 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import htsjdk.variant.vcf.VCFFileReader
import htsjdk.variant.vcf.VCFHeader
import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import scala.collection.SortedMap
-import scala.collection.immutable.SortedSet
import scala.collection.mutable.{ Map, Set }
+import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.JavaConversions._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
+ javaMainClass = getClass.getName
+
+ @Input(doc = "Input vcf files", shortName = "input", required = true)
+ var input: List[File] = Nil
+
+ @Output(doc = "Output fastq files", shortName = "output", required = true)
+ var output: File = _
+
+ @Argument
+ var reference: File = config("reference")
+
+ override def commandLine = super.commandLine +
+ repeat("-I", input) +
+ required("-o", output) +
+ required("-R", reference)
+}
object MergeAlleles extends ToolCommand {
case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null) extends AbstractArgs
--
GitLab