[galaxy-dev] The need for wrappers

Hi, Looking under the tools directory I realized that some tools comes with *_wrapper.py. I wonder under what circumstances is this needed? I'm trying to do a quickie for RepeatMasker. It looks to me like the tool does not allow one to specify the name of the output files. It also appears to me that tools should have an $output variable specifies within the <command> tag. So I was wondering if this is one case where a wrapper.py is needed. Thanks. Timothy