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


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