Yes, phpDocumentor (http://www.phpdoc.org/) is an acceptable standard tool for PHP autodocs. It's the de-facto standard.
It's acceptable to follow the general JavaDoc guidelines for code when documenting PHP code. However, you're going to run into cases where that's not enough because PHP and Java are different languages.
For example, PHP functions have no return type and it's inevitable (and sometimes desirable) for a function to return one type with one context, and another type with in a second context. JavaDoc guidelines aren't going to help with that, because it's impossible to do in Java.