my @script;
GetOptions(
    ...
   'call=s'    => sub { push @script, [ call_method => $_[1] ] },
   'eval=s'    => sub { push @script, [ do_eval     => $_[1] ] },
   'out|o=s'   => sub { push @script, [ output      => $_[1] ] },
   '<>'        => sub { push @script, [ process_tpl => $_[0] ] },
) or pod2usage(2);

...

sub call_method { ... }
sub do_eval     { ... }
sub output      { ... }
sub process_tpl { ... }

# All the global options are taken care of.  Now execute the "script options"
# in the order they were given.
for (@script) {
   my ($method, @args)= @$_;
   $method= main->can($method) or die 'bug';
   $method->(@args);
}