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comparison transformation_wrapper.R @ 3:cc0e9eff0de2 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
author ethevenot
date Wed, 28 Feb 2018 09:15:47 -0500
parents 0ccfc3e15710
children
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2:0ccfc3e15710 3:cc0e9eff0de2
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 library(batch) ## parseCommandArgs 3 library(batch) ## parseCommandArgs
4
5 # Constants
6 argv <- commandArgs(trailingOnly = FALSE)
7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
8 prog.name <- basename(script.path)
9
10 # Print help
11 if (length(grep('-h', argv)) >0) {
12 cat("Usage:", prog.name,
13 "dataMatrix_in myDataMatrixInput.tsv",
14 "method log2|log10|sqrt",
15 "dataMatrix_out myDataMatrixOutput.tsv",
16 "information information.txt",
17 "\n")
18 quit(status = 0)
19 }
4 20
5 source_local <- function(fname){ 21 source_local <- function(fname){
6 argv <- commandArgs(trailingOnly = FALSE) 22 argv <- commandArgs(trailingOnly = FALSE)
7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 23 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
8 source(paste(base_dir, fname, sep="/")) 24 source(paste(base_dir, fname, sep="/"))