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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