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1 ## How to execute this tool
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2 # $Rscript test_norm.R --input input.txt --output output.txt
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3
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4 # Send R errors to stderr
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5 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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6
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7 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9
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10 # Import library
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11 library("getopt")
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12 library(limma)
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13 library("edgeR")
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14
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15 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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16
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17 # Take in trailing command line arguments
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18 args <- commandArgs(trailingOnly = TRUE)
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19
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20 # Get options using the spec as defined by the enclosed list
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21 # Options are read from the default: commandArgs(TRUE)
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22 option_specification = matrix(c(
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23 'input', 'i', 2, 'character',
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24 'output', 'o', 2, 'character'
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25 ), byrow=TRUE, ncol=4);
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26
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27 # Parse options
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28 options = getopt(option_specification);
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29
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30 # Print options to stderr for debugging
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31 cat("\n input: ", options$input)
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32 cat("\n output: ", options$output)
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33
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34 # Read in the input file
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35 inp <- read.table(file = options$input, sep = "\t", header = T, stringsAsFactors = FALSE)
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36
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37 # Changes every value in the first column to 0
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38 cpm <- inp2
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39
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40 # Write output to new file which will be recognized by Galaxy
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41 write.table(cpm, file = options$output, row.names = F, quote = F, sep = "\t")
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42
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43 cat("\n success \n")
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