You can get what you want with something like this:

use warnings;
use strict;

@ARGV == 2 or die "usage: $0 in_filename out_filename\n";

# get first argument, i.e filename
my $in_filename = shift;
print "You chose input <$in_filename>\n";
my $out_filename = shift;
print "You chose output <$out_filename>\n";

#set infile to binary mode
open INFILE, '<:raw', $in_filename or die "can't open $in_filename: $!
+";

open OUTFILE, '>', $out_filename or die "can't open $out_filename: $!"
+;

# read 8 bytes at a time
$/ = \8;

while ( <INFILE> ) {
    print OUTFILE join( ', ', map sprintf( '0x%04x', $_ ), unpack 'S*'
+, $_ ), "\n";
    }
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