Commit 74fa6d37 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs for macs2

parent 05d2e7ea
......@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.macs2
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* General igvtools extension
*
* Created by sajvanderzeeuw on 12/19/14.
*/
abstract class Macs2 extends BiopetCommandLineFunction {
......
......@@ -5,6 +5,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/** Extension for macs2*/
class Macs2CallPeak(val root: Configurable) extends Macs2 {
@Input(doc = "Treatment input", required = true)
var treatment: File = _
......@@ -56,6 +57,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var broadcutoff: Option[Int] = config("broadcutoff")
var callsummits: Boolean = config("callsummits", default = false)
/** Sets output files */
override def beforeGraph: Unit = {
if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
......@@ -67,6 +69,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
output_gapped = new File(outputdir + name.get + ".gappedPeak")
}
/** Returns command to execute */
def cmdLine = {
required(executable) + required("callpeak") +
required("--treatment", treatment) + /* Treatment sample */
......
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