On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>> 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.
> J.

Wouldn't it be better not to have the default value 40 (or 20) in the wrapper
at all? i.e. Leave it out, so that by default that argument isn't used, so that
tophat uses the default it wants to use.

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