[galaxy-dev] advanced parameters: all or nothing?

Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed that when advanced parameters are used, every field is converted and submitted as command line parameter to the tool at runtime. Without changing any of the default values I get a different tophat result than if advanced parameters are left off. I'm curious if the Galaxy team has considered a mechanism for disabling an individual parameter? Or perhaps a way of individually enabling parameters from within the Advanced Parameter block? Just trying to think of a way to use one advanced parameter without using all of them. Cheers, Andrew Warren