Simplest solution I can think of is to have perl run an applescript. You'll have to dig around in the Script Editor.app to find out how to script your application properly. Once you have a working applescript, you can just plug it into the likes of this:

use Mac::AppleScript qw(RunAppleScript);
...
sub run_script {
  my $script;
  my $msg = shift;
  ($script = <<"  EOS") =~ s/^\s+//gm;
    tell application "PDFCompressor"
      ... # more applescript here
    end tell
  EOS
  RunAppleScript( $script ) or die "couldn't run applescript - $!";
}
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s**lil*;  $*=join'',sort split q**;  s;.*;grr; &&s+(.(.)).+$2$1+; $; =
qq-$_-;s,.*,ahc,;$,.=chop for split q,,,reverse;print for($,,$;,$*,$/)
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