I am new to command line usage and don't think this question has been asked elsewhere. I'm trying to adapt an Rscript to be run from the command line in a shell script. Basically, I'm using some tools in the immcantation framework to read and annotate some antibody NGS data, and then to group sequences into their clonal families. To set the similarity threshold, the creators recommend using a function in their shazam package to set an appropriate threshold.
I've made the simple script below to read and validate the arguments:
#!/usr/bin/env Rscript
params <- commandArgs(trailingOnly=TRUE)
### read and validate mode argument
mode <- params[1]
modeAllowed <- c("ham","aa","hh_s1f","hh_s5f")
if(!(mode %in% modeAllowed)){
stop(paste("illegal mode argument supplied. acceptable values are",
paste(paste(modeAllowed, collapse = ", "), ".", sep = ""), "\nmode should be supplied first",
sep = " "))
}
### execute function
cat(threshold)
The script works, however since for each parameter there's only a finite number of options. I was wondering if there was a way of passing in the arguments like --mode aa (for example) from the terminal? All the information I've seen online seems to be using code like my mode <- params[1] from above which I guess only works if the mode argument is first?
