# lots of code, intermingled with lots of pod
...

# Generate html documentation if --makedoc switch is used
my $makedoc  = '';
GetOptions('makedoc' => \$makedoc);

if ($makedoc) {
  makeDoc();
}

# Then, further down
sub makeDoc {
  my $in = "$full_path/myscript.pl";
  my $out = "$full_path/docs/myscript.html";

# Note: updated the above two lines with double-quotes
  
  qx(pod2html --title='$title' --infile=$in --outfile=$out);
}

##</code><code>##

myscript.exe --makedoc