On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren <anwar...@vbi.vt.edu> wrote:
> 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.

That sounds like a bug in the wrapper.

> 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

This should be possible using optional parameters, as of:

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