use strict;
use warnings; 

my @files = map { $_->[0] } 
            sort { $a->[1] cmp $b->[1] ||  $a->[2] <=> $b->[2] } 
            map { [ $_, /\.(\d{12}\-\d{4})/, /.+?-(\d+)\..+$/ ] } <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
abcd1_abc_123456.abc1a_A.201306290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201306290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201305290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201308290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201302290800-0900-3.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-1.gz
abcd1_abc_123456.abc1a_A.201306290800-1000-10.gz
abcd1_abc_123456.abc1a_A.201305290800-1000-11.gz
abcd1_abc_123456.abc1a_A.201308290800-1000-2.gz
abcd1_abc_123456.abc1a_A.201302290800-1000-3.gz