# script.cgi

use CGI;
use BlastTool;

... get info from CGI object ...

BlastTool::do_it(
   $date,
   $show_filter,
   ...
   \@chromo_filter, 
   \@advanced_filter
);

##</code><code>##

# script.pl

use BlastTool;

... prompt the user for the info ...

BlastTool::do_it(
   $date,
   $show_filter,
   ...
   \@chromo_filter, 
   \@advanced_filter
);