Collecting arguments with R

Neel — Fri, 09 Nov 2018 12:21:40 -0600
#! /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="")
BOL: Collecting arguments with R

Collecting arguments with R
