Mercurial > repos > dktanwar > test_r
comparison tmpnt.R @ 0:cc424daed0b0 draft
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| author | dktanwar |
|---|---|
| date | Tue, 24 Oct 2017 07:05:58 -0400 |
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| children |
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| -1:000000000000 | 0:cc424daed0b0 |
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| 1 ## How to execute this tool | |
| 2 # $Rscript test_norm.R --input input.txt --output output.txt | |
| 3 | |
| 4 # Send R errors to stderr | |
| 5 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)}) | |
| 6 | |
| 7 # Avoid crashing Galaxy with an UTF8 error on German LC settings | |
| 8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 9 | |
| 10 # Import library | |
| 11 library("getopt") | |
| 12 library(limma) | |
| 13 library("edgeR") | |
| 14 | |
| 15 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) | |
| 16 | |
| 17 # Take in trailing command line arguments | |
| 18 args <- commandArgs(trailingOnly = TRUE) | |
| 19 | |
| 20 # Get options using the spec as defined by the enclosed list | |
| 21 # Options are read from the default: commandArgs(TRUE) | |
| 22 option_specification = matrix(c( | |
| 23 'input', 'i', 2, 'character', | |
| 24 'output', 'o', 2, 'character' | |
| 25 ), byrow=TRUE, ncol=4); | |
| 26 | |
| 27 # Parse options | |
| 28 options = getopt(option_specification); | |
| 29 | |
| 30 # Print options to stderr for debugging | |
| 31 cat("\n input: ", options$input) | |
| 32 cat("\n output: ", options$output) | |
| 33 | |
| 34 # Read in the input file | |
| 35 inp <- read.table(file = options$input, sep = "\t", header = T, stringsAsFactors = FALSE) | |
| 36 | |
| 37 # Changes every value in the first column to 0 | |
| 38 cpm <- inp2 | |
| 39 | |
| 40 # Write output to new file which will be recognized by Galaxy | |
| 41 write.table(cpm, file = options$output, row.names = F, quote = F, sep = "\t") | |
| 42 | |
| 43 cat("\n success \n") |