Apologies, I didn't see that the file was binary. You're right - my suggestion will only help if your file is tabular. One simple option is to provide an RData to tabular converter for now.
Currently, I think your approach is the best way given the binary dataset. In the future, it'd be nice if dynamic options allowed a function to be used for retrieving options from a dataset. Best, J. On Nov 28, 2012, at 9:39 AM, S. Horsman wrote: > But how does that let me read from a binary file? > > > Bas > > > From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] > Sent: 22 November 2012 15:59 > To: S. Horsman > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] dynamic column names and R ExpressionSet files > > Options and filters should work for what you need: > > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Coption.3E_tag_set > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set > > Best, > J. > > On Nov 22, 2012, at 4:49 AM, S. Horsman wrote: > > > Hi All, > > I'm trying to dynamically load labels from a BioConductor ExpressionSet file > (binary .RData) into a select item type. > This works just fine, but with a few caveats. > > Example (for reference, this is from a modification of > https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.xml): > > <code file="CL_code.py"/> > ... > <page> > <param name="eset" type="data" label="Expression set" format="rdata" > force_select="True" help="An R data file containing an ExpressionSet"/> > </page> > <page> > <param name="label" type="select" > dynamic_options="get_label(eset,False,'class')" force_select="True" > label="Variable to test" size="20" help="Name of the variable subject to > testing" /> ... > > I would like to remove the deprecated page tags here (also then the tool can > be added to a workflow). > However if I do that and then select an ExpressionSet file, the select list > does not update. It only works when loading the page for the first time, or > when I use the page tags. > For text files the solution would be easy; just use type="data_column" and > data_ref="yourinputfileparamname" and it auto-updates the select field > (though not with the actual column names but that is another issue). > With a binary file this is not possible, therefore the dynamic_options > feature is needed to do this. > > Does anyone know of a way to get this to work without using the page tags? > > > Kind regards, > > Bas Horsman > Dept. Bioinformatics > Erasmus MC > > > ___________________________________________________________ > 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/ >
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