# `natsort` from Sort::Key::Natural would be better than `sort`.
# To use this:
# * Install the module,
# * Pass the `-MSort::Key::Natural=natsort` switch to `perl`, and
# * Replace the three instances of `sort` with `natsort`.

perl -lane'
   $data{$F[1]}{$F[2]}{$F[3]} = $F[0];
   ++$cols{$F[3]};
   END {
      local $, = "\t";
      my @cols = sort keys(%cols);
      print undef, undef, @cols;
      for my $x (sort keys(%data)) {
         for my $y (sort keys(%{$data{$x}})) {
            print $x, $y, map { $data{$x}{$y}{$_} } @cols;
         }
      }
   }
'

# Output:
#                 z1      z2
# x1      x1      20
# x1      y1      10      19
# x2      y1      16      12
# x2      y2      15
# y1      y1              11