foreach (@files) {
my $file = $_;

my @newfiles = map { $_->[0] }
  sort { $a->[1] <=> $b->[1] }
  map { [ $_, /.+?-(\d+)\..+$/ ] } @files;

print $_,$/ for @newfiles;

outputs for example:
abcd1_abc_123456.abc1a_A.201307282200-2300-9.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-9.gz
abcd1_abc_123456.abc1a_A.201307272100-2200-10.gz
abcd1_abc_123456.abc1a_A.201307281900-2000-10.gz

I need it to output like this: 
abcd1_abc_123456.abc1a_A.201307282200-2300-1.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-2.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-3.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-4.gz
..etc..
abcd1_abc_123456.abc1a_A.201307282200-2300-10.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-11.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-12.gz

abcd1_abc_123456.abc1a_A.201307282300-2400-1.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-2.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-3.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-4.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-5.gz
..etc..
abcd1_abc_123456.abc1a_A.201307282300-2400-10.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-11.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-12.gz