Neelam Jha
Bioinformatics Beginner
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Collecting arguments with R
By Neelam Jha 2001 days ago
#! /usr/bin/Rscript
## Collect arguments
args <- commandArgs(TRUE)
## Parse arguments (we expect the form --arg=value)
parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
argsL <- as.list(as.character(as.data.frame(do.call("rbind", parseArgs(args)))$V2))
names(argsL) <- as.data.frame(do.call("rbind", parseArgs(args)))$V1
args <- argsL
rm(argsL)
## Give some value to options if not provided
if(is.null(args$opt_arg1)) {args$opt_arg1="default_option1"}
if(is.null(args$opt_arg2)) {args$opt_arg2="default_option1"} else {args$opt_arg2=as.numeric(args$opt_arg2)}
## Default setting when no all arguments passed or help needed
if("--help" %in% args | is.null(args$arg1) | is.null(args$arg2)) {
cat("
The R Script arguments_section.R
Mandatory arguments:
--arg1=type - description
--arg2=type - description
--help - print this text
Optionnal arguments:
--opt_arg1=String - example:an absolute path, default:default_option1
--opt_arg2=Value - example:a threshold, default:10
WARNING : here put all the things the user has to know
Example:
./arguments_section.R --arg1=~/Documents/ --arg2=10 --opt_arg2=8 \n\n")
q(save="no")
}
cat("first mandatory argument : ", args$arg1,"\n",sep="")
cat("second mandatory argument : ", args$arg2,"\n",sep="")
cat("first optional argument : ", args$opt_arg1,"\n",sep="")
cat("second optional argument : ", args$opt_arg2,"\n",sep="")
