Also, note that shell backticks remove the trailing newline, while Perl backticks preserve it.

Given you are just starting with Perl, it is a good idea to sprinkle print statements and error checks in your script to help you understand what is going on. To get you started, try this:

use strict;
use warnings;
my $cmd = '/usr/well561/bin/well.newlogfile';
-f $cmd or die "error: '$cmd' not found";
-x $cmd or die "error: '$cmd' not executable";
my $out = `$cmd 1`;
my $rc = $? >> 8;
print "command exit code is $rc\n";
$rc == 0 or warn "warning: command returned $rc\n";
chomp $out;    # remove trailing new line from command output
print "command output:$out:\n";
if ($out eq 'Y')
{
   print "command returned Y\n";
}
[download]

Study the script above, referring to the Perl documentation, and you should be on your way to rewriting your old shell scripts in Perl. As for learning Perl, take a look at learn.perl.org and Perl Tutorial Hub. Good luck!