Commit cfe22b5c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed RepSet

parent 913cb591
......@@ -24,7 +24,9 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
@Input(required = false)
var reference_seqs_fp: Option[File] = config("reference_seqs_fp")
var outputDir: File = _
@Input(required = false)
var fastaInput: Option[File] = None
var sortBy: Option[String] = config("sort_by")
def versionCommand = executable + " --version"
......@@ -34,9 +36,9 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
def cmdLine = executable +
required("-i", inputFile) +
optional("-f", outputFasta) +
required("-o", outputFasta) +
optional("-m", rep_set_picking_method) +
required("-o", outputDir) +
optional("-f", fastaInput) +
optional("-l", logFile) +
optional("-s", sortBy) +
optional("-r", reference_seqs_fp)
......
......@@ -38,10 +38,10 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
add(pickOtus)
val pickRepSet = new PickRepSet(this)
pickRepSet.outputDir = new File(outputDir, "pick_rep_set")
val repSetOutputDir = new File(outputDir, "pick_rep_set")
pickRepSet.inputFile = pickOtus.otusTxt
pickRepSet.outputFasta = Some(new File(pickRepSet.outputDir, fastaR1.getName))
pickRepSet.logFile = Some(new File(pickRepSet.outputDir, fastaR1.getName
pickRepSet.outputFasta = Some(new File(repSetOutputDir, fastaR1.getName))
pickRepSet.logFile = Some(new File(repSetOutputDir, fastaR1.getName
.stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna") + ".log"))
add(pickRepSet)
......
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