> 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.

Recent Tophat versions have changed parameters and default values again. I made 
the following changes in 3bd8bed55631 to make the wrapper compatible with 
Tophat 1.4.0:

*removed junctions_filter parameter
*changed the default value for max-mismatches from 40 to 20

This should ensure that enabling advanced parameters but leaving them untouched 
yields the same results as using default parameters.

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