Commit 57ad3610 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing some bugs

parent ef878d64
......@@ -9,7 +9,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 4
override def versionCommand = executable + " -v"
override val versionRegex = """.*version \w* .*""".r
override val versionRegex = """.*version ([\w\.]*) .*""".r
@Input(doc = "Input phy/fasta file", required = true)
var input: File = _
......@@ -32,8 +32,8 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
@Argument(doc = "Name of output files", required = true)
var f: String = "d"
@Argument(doc = "Output directory", required = false)
var w: String = jobLocalDir.getAbsolutePath
@Argument(doc = "Output directory", required = true)
var w: String = _
@Input(required = false)
var t: File = _
......@@ -51,6 +51,8 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
f match {
case "d" if b.isEmpty => out +:= getBestTree
case "d" if b.isDefined => out +:= getBootstrap
case "b" => out +:= new File(w + "/out.out")
case _ =>
}
}
......
......@@ -57,7 +57,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add(raxmlMl)
val raxmlBoot = new Raxml(this)
raxmlMl.input = input
raxmlBoot.input = input
raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBoot.p = config("seed", default = seed)
raxmlBoot.b = config("seed", default = seed)
......@@ -66,11 +66,12 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add(raxmlBoot)
val raxmlBi = new Raxml(this)
raxmlMl.input = input
raxmlBi.input = input
raxmlBi.t = raxmlMl.getBestTree
raxmlBi.z = raxmlBoot.getBootstrap
raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlBi.p = config("seed", default = seed)
raxmlBi.f = "b"
raxmlBi.n = outputName + "_bi"
raxmlBi.w = outputDir
add(raxmlBi)
......
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