Commit 15cd85a4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added extension for clased reference otu picking

parent d222ab7e
package nl.lumc.sasc.biopet.extensions.qiime
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 12/4/15.
*/
class PickClosedReferenceOtus(val root: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "pick_closed_reference_otus.py")
@Input(required = true)
var inputFasta: File = _
var outputDir: File = null
override def defaultThreads = 2
override def defaultCoreMemory = 5.0
def versionCommand = executable + " --version"
def versionRegex = """Version: (.*)""".r
@Input(required = false)
var parameter_fp: Option[File] = config("parameter_fp")
@Input(required = false)
var reference_fp: Option[File] = config("reference_fp")
@Input(required = false)
var taxonomy_fp: Option[File] = config("taxonomy_fp")
var assign_taxonomy: Boolean = config("assign_taxonomy", default = false)
var force: Boolean = config("force", default = false)
var print_only: Boolean = config("print_only", default = false)
var suppress_taxonomy_assignment: Boolean = config("suppress_taxonomy_assignment", default = false)
def cmdLine = executable +
required("-i", inputFasta) +
required("-o", outputDir) +
optional("--reference_fp", reference_fp) +
optional("--parameter_fp", parameter_fp) +
optional("--taxonomy_fp", taxonomy_fp) +
conditional(assign_taxonomy, "--assign_taxonomy") +
conditional(force, "--force") +
conditional(print_only, "--print_only") +
conditional(suppress_taxonomy_assignment, "--suppress_taxonomy_assignment") +
(if (threads > 1) required("-a") + required("-O", threads) else "")
}
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