One pretty standard way is to just pass the file(s) on the command line and parse each file one after the next:

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

GetOptions(
    'id1=s' => \my $id1,
    'id2=s' => \my $id2,
);

for my $file (@ARGV) {
    open (my $filename, "<", $file) or die "Could not open $file, $!";

    while (<$filename>){
        while (/$id1/g && /$id2/g)
        {
            print "$file:$.\n";
        }
    }

    close ($filename);
}
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Called like:

script.pl --id1="test1|test2" --id2="test3|test4" file1.txt file2.txt
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Regarding your glob problem, post a small sample of your input file so others can reproduce the issue.