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_ba...
-- jt
On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann Ann.Gomez@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 Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.gomez@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada
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