Ann,

I think you may be able to do this by generating another nexus file
using "configfiles" in the Galaxy tool config which just contains a
command block, similar to the example here:

  
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F

-- jt


On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann <ann.go...@agr.gc.ca> wrote:
> Hello all,
>
>
>
> I’ve written a MrBayes wrapper that accepts a Nexus file (presumably
> containing a data block and a command block). In order to make it a bit
> easier for new users, I was hoping to be able to  let users specify some
> parameters, such as their model, in Galaxy, as opposed to including it in
> the command block of the Nexus file. Am I correct in thinking this is not
> possible since MrBayes does not have a way to invoke commands in-line?
>
>
>
> To clarify for non-MrBayes people, my limited understanding is that you
> either invoke  the interpreter with “$ mb” and then enter your commands, or
> directly execute a Nexus file (containing the data and commands) with “ $ mb
> <nexusfilename>”.
>
>
>
> Please correct me if I’m missing something or thinking about this completely
> wrong. I’d appreciate any input about MrBayes or a similar kind of tool.
>
>
>
> Cheers,
>
> Ann
>
>
>
> Ann Gomez
>
> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
>
> KW Neatby Bldg | éd. KW Neatby
> 960 Carling Ave| 960, avenue Carling
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> E-mail Address / Adresse courriel: ann.go...@agr.gc.ca
> Telephone | Téléphone 613-759-6805
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> Government of Canada | Gouvernement du Canada
>
>
>
>
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