--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/test-Maaslin/test-Maaslin.R	Tue May 13 22:00:40 2014 -0400
@@ -0,0 +1,41 @@
+c_strDir <- file.path(getwd( ),"..")
+
+source(file.path(c_strDir,"lib","Constants.R"))
+strTestingDirectory = file.path(c_strDir,c_strTestingDirectory)
+sScriptMaaslin = file.path( c_strDir, "Maaslin.R" )
+
+context("Test Run From Commandline")
+
+#Input Files
+sTestReadConfig = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.read.config")
+sTestCustomR = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.R")
+sTestMaaslinDirectory = file.path(strTestingDirectory, c_strTemporaryFiles, "testMaaslin")
+sTestOutput = file.path(sTestMaaslinDirectory,"TestMaaslin_Summary.txt")
+sTestTSV = file.path(strTestingDirectory, c_strTestingInput, "TestMaaslin.tsv")
+#Test file answers
+sTestOutputAnswer = file.path(strTestingDirectory, c_strCorrectAnswers, "TestMaaslin.tsv")
+
+#Delete Test MaAsLin output
+unlink(sTestMaaslinDirectory, recursive=TRUE)
+#Make neccessary directories
+dir.create(sTestMaaslinDirectory)
+dir.create(file.path(sTestMaaslinDirectory,"QC"))
+
+sCommand = paste(sScriptMaaslin, "-v", "ERROR", "-d", "0.25", "-r", "0.0001", "-p", "0.1", sTestOutput, sTestTSV, sTestReadConfig, sTestCustomR, sep=" ")
+print(sCommand)
+system(sCommand)
+
+sExpectedTitle = "\tVariable\tFeature\tValue\tCoefficient\tN\tN.not.0\tP.value\tQ.value"
+iExpectedNumberOfLines = 3
+lsOutputSummaryFile = readLines(sTestOutput)
+
+test_that("Make sure that the summary output file is what is expected (generally).",{
+  expect_equal(lsOutputSummaryFile[1], sExpectedTitle)
+  expect_equal(length(lsOutputSummaryFile),iExpectedNumberOfLines)
+})
+
+lsDirectoryStructure = list.files(sTestMaaslinDirectory)
+lsDirectoryStructureAnswer = c(basename(sTestOutput),"QC","TestMaaslin-age.pdf","TestMaaslin-age.txt","TestMaaslin-dx.txt","TestMaaslin.pdf","TestMaaslin.txt")
+test_that("Make sure the expected directory structure is created.",{
+  expect_equal(sort(lsDirectoryStructure), sort(lsDirectoryStructureAnswer))
+})