--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tmpnt.R	Tue Oct 24 07:05:58 2017 -0400
@@ -0,0 +1,43 @@
+## How to execute this tool
+# $Rscript test_norm.R --input input.txt --output output.txt
+
+# Send R errors to stderr
+options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# Import library
+library("getopt")
+library(limma)
+library("edgeR")
+
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+# Get options using the spec as defined by the enclosed list
+# Options are read from the default: commandArgs(TRUE)
+option_specification = matrix(c(
+  'input', 'i', 2, 'character',
+  'output', 'o', 2, 'character'
+), byrow=TRUE, ncol=4);
+
+# Parse options
+options = getopt(option_specification);
+
+# Print options to stderr for debugging
+cat("\n input: ", options$input)
+cat("\n output: ", options$output)
+
+# Read in the input file
+inp <- read.table(file = options$input, sep = "\t", header = T, stringsAsFactors = FALSE)
+
+# Changes every value in the first column to 0
+cpm <- inp2
+
+# Write output to new file which will be recognized by Galaxy
+write.table(cpm, file = options$output, row.names = F, quote = F, sep = "\t")
+
+cat("\n success \n")