use strict;
use warnings;

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

print $_,$/ for @files;

__DATA__
abcd1_abc_123456.abc1a_A.201307290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-3.gz