--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_wilcoxon_test.R	Thu Apr 21 04:21:13 2016 -0400
@@ -0,0 +1,55 @@
+library('getopt')
+
+option_specification = matrix(c(
+  'input_file', 'a', 2, 'character',
+  'output_file', 'b', 2, 'character',
+  'column1_id', 'c', 2, 'integer',
+  'column2_id', 'd', 2, 'integer',
+  'alternative','e',2,'character',
+  'paired','f',2,'logical',
+  'exact','g',2,'logical',
+  'correct','h',2, 'logical',
+  'mu','i',2,'integer',
+  'header','y',2,'logical'
+), byrow=TRUE, ncol=4);
+
+options = getopt(option_specification);
+
+header = TRUE
+if(!is.null(options$header)) header = options$header
+
+data = read.table(options$input_file, sep = '\t', h = header)
+
+column1_id = 1
+if(!is.null(options$column1_id)) column1_id = options$column1_id
+x = data[,column1_id]
+y = NULL
+if(!is.null(options$column2_id)) y = data[,options$column2_id]
+
+alternative = 'two.sided'
+if(!is.null(options$alternative)) alternative = options$alternative
+
+mu = 0
+if(!is.null(options$mu)) mu = options$mu
+
+paired = FALSE
+if(!is.null(options$paired)) paired = options$paired
+
+exact = NULL
+if(!is.null(options$exact)) exact = options$exact
+
+correct = TRUE
+if(!is.null(options$correct)) correct = options$correct
+
+test = wilcox.test(x = x, y = y, alternative = alternative, mu = mu, 
+    paired = paired, exact = exact, correct = correct)
+
+m = matrix(ncol = 2, nrow = 6)
+m[1,] = c('statistic',test$statistic)
+m[2,] = c('parameter',test$parameter)
+m[3,] = c('p.value',test$p.value)
+m[4,] = c('null.value',test$null.value)
+m[5,] = c('alternative',test$alternative)
+m[6,] = c('method',test$method)
+write.table(m, file = options$output_file, sep = "\t", quote = FALSE, 
+    row.names = FALSE, col.names = FALSE)