# R_argument_pass_test.r

# Load arguments and print the script usage information
args = commandArgs(trailingOnly=TRUE)
cat("
#Rscript --vanilla yourScript.R [arg1] [arg2] [arg3]
#arg1: sample table (the column name p_id is neeeded for argument 2)
#arg2: project id (must be one of value in the p_id column of the sample table)
#arg3: output file path 
")
# Test if there are three argument: if not, return an error
if (length(args)!=3) {
  stop("Three arguments must be supplied (input).n", call.=FALSE)
}
# Test the argument is correctly passed into R
#print(length(args)) # it should be 3
#print(args[1])      # the first argument
#print(args[2])      # the second argument
#print(args[3])      # the third  argument

###### tags: `R template`