Just accept parameters via @ARGV
.
Your script should open with:
use strict;
use warnings;
use autodie;
die "Usage: $0 Input_File Output_File\n" if @ARGV != 2;
my ($infile, $outfile) = @ARGV;
And later in your file
open (F, '<', $infile);
# ...
open (F1,'>>', $outfile);