XOOPS uses PHPDoc as a document system. Both Doxygen and PHPDoc can handle document tags of javadoc. But, each document systems have some original rules. And, because Doxygen has been developed for C and C++, Doxygen may not be able to generate goodly documents for PHP programs.
However, Doxygen might be easy to use for you than PHPDoc. I like the generated document by Doxygen, than PHPDoc. In XOOPS Cube, we shouldn't use the original tag of Doxygen. So the generated document doesn't include the maximum impact of Doxygen, but it's enough.
Let's try out. At first, checkout the latest version from CVS. You may reference this article in XOOPS Cube Gems, to do it. Next, download Doxygen and install it.
At next entry, you will generate documents by these software. See you tomorrow.