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.

Andrew Warren
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