Hi Ross,

That's excellent, thanks for jumping in!

I've been charged with constructing a Galaxy tool kit for basic microarray data 
analysis for my group's Galaxy instance, and I looked at your Rgenetics / 
Rexpression (more the latter of course) as a starting point.  I was wondering 
how the compatibility of your tools and datatypes with plain old galaxy-dist is 
going these days.  I've wound up rewrapping or rewriting some of your tools 
because they didn't seem to be working out of the box.  Minor path problems 
weren't hard to fix.  More major problems had to do with incomplete / broken 
ways that the Galaxy core handles composite datasets.

So I'm wondering if you've kept up active development over the last few months 
and found good workarounds.  (I don't want to hijack this thread, so perhaps a 
private reply or a new thread makes sense.)

Best,
Eric

________________________________
From: Ross [ross.laza...@gmail.com]
Sent: Thursday, November 17, 2011 8:47 PM
To: Paniagua, Eric
Cc: Timothy Wu; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Name your own tool's output?

Hi Timothy, if by "customize the name of the output" you mean "display a string 
of my choice as the new history item display name" then yes.

Eric - thanks for reminding me to fix that old code!
:)

Post execution hooks are not needed - there's a much cleaner way - eg given a 
form field "usersuppliedlabel", something like
<outputs>
    <data format="foo" name="output"  label="$usersuppliedlabel">
 ...
The label becomes the history item display name if that helps?

On Thu, Nov 17, 2011 at 8:26 PM, Paniagua, Eric 
<epani...@cshl.edu<mailto:epani...@cshl.edu>> wrote:
Hi Timothy,

Check out tools/rgenetics/rgLDIndep.xml and the associated 
tools/rgenetics/rgLDIndep_code.py for an example of how to change the name of 
your output data.

Best,
Eric

________________________________
From: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>]
 on behalf of Timothy Wu [2hug...@gmail.com<mailto:2hug...@gmail.com>]
Sent: Wednesday, October 12, 2011 4:51 AM
To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Name your own tool's output?

Hi,

I thought I had already asked this question a while ago, but I can't find it so 
I guess I haven't.

When porting my own tool, is there anyway to customize the name of the output?

Timothy

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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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