One way, using Getopt::Long, is to use an array and to die if the array has more than one element:

use warnings;
use strict;
use Getopt::Long;

my @in;
GetOptions('input=s', \@in) or die;
die "Error: cant have multiple inputs" if @in > 1;
print "input = @in\n";
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UPDATE: There is another solution at: http://stackoverflow.com/questions/10045067/can-getoptlong-getoptions-generate-an-error-if-the-same-option-occurs-multiple