# NOTE! this is only a general outline of the concept,
# and is NOT actual working code.

# wrapper.pl

use strict;
use warnings;

my $flagfile = '/path/to/flag_file.txt';

# you might want to test and see if this exists first, indicating a possible
# failure in code elsewhere.
#
# also, you might write the PID of the current process into the file so you
# can check later if the process is still running if the file is present.
open my $flag, '>', $flagfile;
close $flag;

my @script_params = (
  '-opt1 yes',
  '-opt2 no',
);

my $script = '/path/to/script.pl';

# use the multi-arg version of system to avoid lot's of gotchas. RTF(ine)M.
system( $script, @script_params );

rm $flagfile;

exit;