[galaxy-user] why the result files are empty ? and is java applet supported by galaxy system?

Hi All, We want to add a program “PhyML 3.0” to galaxy system. This software was for phylogenetic developed byhttp://www.atgc-montpellier.fr/phyml/binaries.php.It can run normally in Linux environment with a file for example named “sample” as input and two files automatically named “sample.phy_phyml_stats.txt” and “sample.phy_phyml_tree.txt” as outputs. However, after added it to galaxy system, we found that it can produce the right result files in directory "/var/we/galaxy-dist/database/files/000”, but they did not return to the web page where they are empty. So who can tell me what is wrong? Another question, is java applet supported by galaxy system? Thank you very much! Best Wishes! Yan-Hui Li