sub MyModuule::DoTheCgiDance {
    my $query = CGI->new; ## FORMDATA
    my( $headers, $body ) = DoTheDance( $query );
    print $headers, $body;
}
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So for commandline version you might have

...
use MyModuule;
MyModuule::DoTheCLIDance( @ARGV );
exit( 0 );
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where

sub MyModuule::DoTheCLIDance {
    my %args  = GetOptMyArgsIWant(\@_);
    my $query = CGI->new( %args ); ## FORMDATA
    my( $headers, $body ) = DoTheDance( $query );
    print $body; ## no headers on CLI :)
}
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and the other cgi

sub MyModuule::DoTheCgiDanceOTHER {
   my $query = CGI->new;
   my( $headers, $body ) = PutOnSomePants( $query );
   print $headers, $body;
}

sub MyModuule::DoTheCLIDanceOTHER {
## no advanced getopt stuff
## just key value key value key value
   my $query = CGI->new( @_ );
   my( $headers, $body ) = PutOnSomePants( $query );
   print $body;
}
[download]

The idea is each .cgi or .pl, uses some modules and calls calls one subroutine to take care of everything