Added basic trait for basis of all pipeline templates

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.{ Question, ToolCommand }
+
+/**
+  * Created by pjvanthof on 17/12/2016.
+  */
+trait TemplateTool extends ToolCommand {
+  import TemplateTool._
+  case class Args(expert: Boolean = false) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[Unit]("expert") valueName "<file>" action { (x, c) =>
+      c.copy(expert = true)
+    } text "Path to input file"
+  }
+
+  /**
+    * Program will split fastq file in multiple fastq files
+    *
+    * @param args the command line arguments
+    */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    val standard: Map[String, Any] = Map("output_dir" -> Question.askValue("Output directory", validation = List(isAbsolutePath, parentIsWritable)))
+    pipelineMap(standard, cmdArgs.expert)
+  }
+
+  def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any]
+
+}
+
+object TemplateTool {
+  def isAbsolutePath(value: String): Boolean = {
+    if (new File(value).isAbsolute) true else {
+      println(s"'$value' must be a absulute path")
+      false
+    }
+  }
+
+  def mustExist(value: String): Boolean = {
+    if (new File(value).exists()) true else {
+      println(s"'$value' does not exist")
+      false
+    }
+  }
+
+  def parentIsWritable(value: String): Boolean = {
+    val parent = new File(value).getParentFile
+    if (!parent.exists()) {
+      println(s"$parent does not exist")
+      false
+    } else if (!parent.canRead) {
+      println(s"No premision to read $parent")
+      false
+    } else if (!parent.canWrite) {
+      println(s"No premision to write $parent")
+      false
+    } else true
+  }
+}
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