CGIs derive their parameters from either $ENV{'QUERY_STRING'} or <STDIN> (or both!), while Getopt::Long expects everything to be in @ARGV.

Converting one to the other is trivial ...

my $extract;
my $file;
{
    local @ARGV = split /&/, $ENV{'QUERY_STRING'};

    GetOptions(
        'file=s'   => \$file,
        'extract!' => \$extract,
    );
}
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That'll break if you have URI-escaped characters (ie, %7E instead of ~), so a more robust solution would be to iteratively build @ARGV using CGI's param funcs.

my $extract;
my $file;
{
    local @ARGV;

    foreach my $key ( param ) {
        if ( param($key) ) {
            foreach my $value ( param($key) ) {
                push @ARGV, $key, $value;
            }
        } else {
              # arg-less booleans
            push @ARGV, $key;
        }
    }

    GetOptions(
        'file=s'   => \$file,
        'extract!' => \$extract,
    );
}
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