If you know that the first two arguments you'll get are the XML file and the output file then you can do something like this:

#!/usr/bin/perl -w

use strict;
use Getopt::Std;
use Data::Dumper;

my %switches;

%switches = splice(@ARGV, 0, 4);

# parse the XML file and work out what other arguments
# you're going to be passed. Use that info to build $fmt
my $fmt = 'd:m:';

getopts($fmt, \%switches);

foreach (keys %switches) {
  $switches{$_} = [ split /\s+/, $switches{$_} ];
}

print Dumper \%switches;
[download]

It's a bit fragile tho' as it assumes there will be spaces between the first two options and their arguments.

--
<http://www.dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg