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.goecks@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:
 
 
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


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