The PerlTidy manpage doesn't mention chained methods so I guess it doesn't handle them.

As a workaround you could format the code manually and then tell it to ignore that block with PerlTidy --format-skipping (#<<< #>>>) comments:

    #<<<
    my $res = SOAP::Lite
        ->autotype(0)
        ->uri('http:....')
        ->proxy('http:...')
        ->function_call();
    #>>>
[download]

Of course if you have hundreds of instances like this then that will quickly become a pain.

You can also force alignment by using comments at the end of each line or newlines between them (but neither of those has much advantage over the above):

    my $res = SOAP::Lite       #
      ->autotype( 0 )          #
      ->uri( 'http:....' )     #
      ->proxy( 'http:...' )    #
      ->function_call();       #
[download]

--
John.