Further to John's answer, Getopt::Std may be of use to you. I pass options in as follows:

use strict;
use Getopt::Std;
my $USAGE="USAGE: sample.pl -f <infile1> -i <infile2> -o <outfile>";
my %Options;
getopts('f:i:o:', \%aOptions);
my $infile1= $aOptions{f} || die "** $USAGE.\nERROR missing input file
+1 ** ";
my $infile2= $aOptions{i} || die "** $USAGE.\nERROR missing input file
+2 ** ";
my $outfile= $aOptions{o} || die "** $USAGE.\nERROR missing output fil
+e ** ";
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