Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much 
appreciated! 

Ann


-----Original Message-----
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor
Sent: Monday, October 29, 2012 2:03 PM
To: Gomez, Ann
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

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
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> of Canada | Gouvernement du Canada
>
>
>
>
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