Your perfectly working script is very scary and needlessly convoluted. But to answer your question: open a file, read its lines into an array, make sure the values are chomped and use that array instead of @ARGV (or cheat and put everything in @ARGV directly).

I think the easiest way to do this is by using simple oneliners. Under unixish systems (where \r is always just CR), I use:

perl -i -pe's/\r//' file file ...  # do-to-unix
[download]

and

perl -i -pe's/$/\r/' file file ...  # unix-to-dos
[download]

Or, no, this is not the easiest way. The easiest way is to use the dos2unix and unix2dos tools.