RefflatStats.scala 1.86 KB
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/**
  * Biopet is built on top of GATK Queue for building bioinformatic
  * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
  * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
  * should also be able to execute Biopet tools and pipelines.
  *
  * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
  *
  * Contact us at: sasc@lumc.nl
  *
  * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
package nl.lumc.sasc.biopet.extensions.tools

import java.io.File

import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}

/**
  *
  */
class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Reference {
  def toolObject = nl.lumc.sasc.biopet.tools.refflatstats.RefflatStats

  @Input(required = true)
  var reference: File = _

  @Input(required = true)
  var refflatFile: File = _

  @Output(required = true)
  var geneOutput: File = _

  @Output(required = true)
  var transcriptOutput: File = _

  @Output(required = true)
  var exonOutput: File = _

  @Output(required = true)
  var intronOutput: File = _

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  override def defaultCoreMemory = 5.0

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  override def beforeGraph(): Unit = {
    super.beforeGraph()
    if (reference == null) reference = referenceFasta()
  }

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  override def cmdLine: String =
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    super.cmdLine +
      required("-a", refflatFile) +
      required("-R", reference) +
      required("-g", geneOutput) +
      required("-t", transcriptOutput) +
      required("-e", exonOutput) +
      required("-i", intronOutput)
}