From 74f96c8000900e3ce5e60c05439dacba555ffd67 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 31 Oct 2014 16:02:24 +0100
Subject: [PATCH] Added RAxml extension
---
.../lumc/sasc/biopet/extensions/Raxml.scala | 71 +++++++++++++++++++
1 file changed, 71 insertions(+)
create mode 100644 biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
new file mode 100644
index 000000000..a92926381
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -0,0 +1,71 @@
+package nl.lumc.sasc.biopet.extensions
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.File
+
+class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
+
+ override val defaultThreads = 4
+ override def versionCommand = executable + " -v"
+ override val versionRegex = """.*version \w* .*""".r
+
+ @Input(doc = "Input phy/fasta file", required = true)
+ var input: File = _
+
+ @Argument(doc = "Model", required = true)
+ var m: String = _
+
+ @Argument(doc = "Parsimony seed", required = false)
+ var p: Option[Int] = config("p")
+
+ @Argument(doc = "Bootstrapping seed", required = false)
+ var b: Option[Int] = config("b")
+
+ @Argument(doc = "Number of runs", required = false)
+ var N: Option[Int] = config("N")
+
+ @Argument(doc = "Name of output files", required = true)
+ var n: String = _
+
+ @Argument(doc = "Name of output files", required = true)
+ var f: String = "d"
+
+ @Argument(doc = "Output directory", required = false)
+ var w: String = jobLocalDir.getAbsolutePath
+
+ @Input(required = false)
+ var t: File = _
+
+ @Input(required = false)
+ var z: File = _
+
+ @Output(doc = "Output files", required = false)
+ private var out: List[File] = Nil
+
+ executable = config("exe", default = "raxmlHPC")
+
+ override def afterGraph {
+ super.afterGraph
+ f match {
+ case "d" if b.isEmpty => out +:= getBestTree
+ case "d" if b.isDefined => out +:= getBootstrap
+ }
+ }
+
+ def getBestTree: File = new File(w + File.separator + "RAxML_bestTree." + n)
+ def getBootstrap: File = new File(w + File.separator + "RAxML_bootstrap." + n)
+
+ def cmdLine = required(executable) +
+ required("-m", m) +
+ required("-s", input) +
+ optional("-p", p) +
+ optional("-b", b) +
+ optional("-N", N) +
+ optional("-w", w) +
+ optional("-f", f) +
+ optional("-t", t) +
+ optional("-z", z) +
+ (if (threads > 1) required("-T", threads) else "")
+}
\ No newline at end of file
--
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