Well I tried a very basic example:

#!/usr/bin/perl

use strict;
use warnings;

print "Please enter an output file name: ";
my $outputfile = <STDIN>;
chomp($outputfile);
print "User input: $outputfile\n";
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and converted it to an executable using pp:

pp -o inputtest inputtest.pl
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Which runs as follows:

Please enter an output file name: testfile.txt
User input: testfile.txt
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Perhaps if you showed an example of your code and how you converted it to an executable someone would be able to help.