Two possible solutions:

The first one involves making the correct expansion in the call:

perl ./script.pl $(ls *.txt | sed 's/^/-file /')
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This converts the call to:

perl ./script.pl -file myfile.txt -file yourfile.txt -file ourfile.txt
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But this is ugly, isn't it?

Another solution is to do the expansion inside of the script:

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long qw (GetOptions);

my (@Files);

Getopt::Long::Configure("no_ignore_case", "prefix_pattern=(--|-|\/)");
GetOptions ("file=s@" => \@Files);

my @globs = map {glob ($_)} @Files;
print "glob: $_\n" for @globs;
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Now you can call the script like:

./script.pl -file "*.txt"
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And get the expected output. The quotes in the call arount *.txt are needed to prevent the expansion in the shell prior to the actual call to the script.

./script.pl -file "*.txt"
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myfile.txt
yourfile.txt
ourfile.txt
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./script.pl -file myfile.txt -file yourfile.txt -file ourfile.txt
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myfile.txt
yourfile.txt
ourfile.txt
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HTH

citromatik