Mercurial > repos > melpetera > tablemerge
diff tablemerge_wrap.R @ 0:19e19f40dc7a draft
Test the tool dependencies managing.
| author | melpetera |
|---|---|
| date | Tue, 26 Jul 2016 08:28:03 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tablemerge_wrap.R Tue Jul 26 08:28:03 2016 -0400 @@ -0,0 +1,38 @@ +#!/usr/bin/Rscript --vanilla --slave --no-site-file + +################################################################################################ +# WRAPPER FOR tablemerge_script.R (TABLE MERGE) # +# # +# Author: Melanie PETERA # +# User: Galaxy # +# Original data: used with tablemerge_script.R # +# Starting date: 11-05-2015 # +# V-1: Firt version of wrapper # +# # +# # +# Input files: dataMatrix ; Metadata file # +# Output files: dataMatrix ; Metadata file # +# # +################################################################################################ + + +library(batch) #necessary for parseCommandArgs function +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects + +source_local <- function(...){ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))} +} +#Import the different functions +source_local("tablemerge_script.R","RcheckLibrary.R","miniTools.R") + + +if(length(args) < 4){ stop("NOT enough argument !!!") } + + +tab.merge(args$dataMatrix_in, args$Metadata_in, args$metatype, args$combined_out) + + +#delete the parameters to avoid the passage to the next tool in .RData image +rm(args)