Hi Eric, I have no current resources or active users for microarray development so I can't contribute much and although the rgenetics code works fine with galaxy central the rexpression code is way out of date - which is why the metadata handling is so broken. There are ongoing problems in galaxy central with composite objects - downloads, pages and other things have been broken for a long time - so fixes would definitely be welcome. As far as the design goes, the challenge is representing complex R objects like expressionsets in Galaxy. The composite representation is a complex solution with the advantage that the pheno data is available for the user to (eg) select variables for limma - which would otherwise not be very convenient in a Galaxy tool form which can't go into R to read the phenoData slot. I'd be very happy to see the project continue so will provide whatever help I can... On Fri, Nov 18, 2011 at 10:50 AM, Paniagua, Eric <epaniagu@cshl.edu> wrote:
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.lazarus@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 <epaniagu@cshl.edu<mailto:epaniagu@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-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu>] on behalf of Timothy Wu [2huggie@gmail.com<mailto:2huggie@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;
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;