Adding basic unit tests

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

+package nl.lumc.sasc.biopet.core
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 09/09/15.
+ */
+class BiopetPipeTest extends TestNGSuite with Matchers {
+  class Pipe1 extends BiopetCommandLineFunction {
+    val root = null
+    def cmdLine = "pipe1" +
+      (if (!inputAsStdin) " input1 " else "") +
+      (if (!outputAsStsout) " output1 " + "")
+  }
+
+  class Pipe2 extends BiopetCommandLineFunction {
+    val root = null
+    def cmdLine = "pipe2" +
+      (if (!inputAsStdin) " input2 " else "") +
+      (if (!outputAsStsout) " output2 " + "")
+  }
+
+  @Test def testPipeCommands: Unit = {
+    val pipe1 = new Pipe1
+    val pipe2 = new Pipe2
+    pipe1.commandLine.contains("pipe1") shouldBe true
+    pipe1.commandLine.contains("input1") shouldBe true
+    pipe1.commandLine.contains("output1") shouldBe true
+    pipe2.commandLine.contains("pipe2") shouldBe true
+    pipe2.commandLine.contains("input2") shouldBe true
+    pipe2.commandLine.contains("output2") shouldBe true
+  }
+
+  @Test def testPipe: Unit = {
+    val pipe = new Pipe1 | new Pipe2
+    pipe.commandLine.contains("pipe1") shouldBe true
+    pipe.commandLine.contains("input1") shouldBe true
+    pipe.commandLine.contains("output1") shouldBe false
+    pipe.commandLine.contains("pipe2") shouldBe true
+    pipe.commandLine.contains("input2") shouldBe false
+    pipe.commandLine.contains("output2") shouldBe true
+  }
+}