Hi Ann, Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator), Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST uses an input xml file that it can parse to execute the analysis. Garli can take a config file that's generated by the Galaxy from the options a user selects in the interface. RAxML is a more traditional command-line application albeit with very convoluted combinations of inputs and outputs that change on every release, which is why my wrapper only supports RAxML 7.3.2. Galaxy provides a lot of choices for handling the applications inputs. MrBayes in this regard is most similar to Garli, so you can take a look at that wrapper. You can take the options from the Galaxy mrbayes interface and write them to a config file that can be fed to MrBayes as a separate NEXUS file just as the Chapter 5 "How do I run MrBayes in batch mode?" of the MrBayes manual describes.
Regards, Alex On Oct 29, 2012, at 2:03 PM, James Taylor <ja...@jamestaylor.org> wrote: > 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 >> Ottawa, ON | Ottawa (ON) K1A 0C6 >> E-mail Address / Adresse courriel: ann.go...@agr.gc.ca >> Telephone | Téléphone 613-759-6805 >> Facsimile | Télécopieur 613-759-1701 >> Government of Canada | Gouvernement du Canada >> >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
