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
On Wed, Oct 12, 2011 at 4:50 PM, Timothy Wu <2huggie@gmail.com> wrote:
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
I have another perhaps related question. If my tool A have variable number of outputs no known till tool run, but the next tool B in pipeline requires a couple of designated outputs (not all) from tool A, is there a way to specify this in the workflow? In another word, A has various different type of output, and I want some output file from A to go into this particular input file field in B. I though this might be related to my prior question. Timothy
Hi Timothy I don't really see the connection to you first question, but maybe I misunderstood the first one.... Anyway, you probably need to define those output files which are required by "B" as 'Static Multiple Outputs' and the rest as 'Variable Static Outputs determined by parameter values'. Again, see the wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files Regards, Hans On 10/12/2011 11:02 AM, Timothy Wu wrote:
On Wed, Oct 12, 2011 at 4:50 PM, Timothy Wu<2huggie@gmail.com> wrote:
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
I have another perhaps related question. If my tool A have variable number of outputs no known till tool run, but the next tool B in pipeline requires a couple of designated outputs (not all) from tool A, is there a way to specify this in the workflow? In another word, A has various different type of output, and I want some output file from A to go into this particular input file field in B.
I though this might be related to my prior question.
Timothy
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Timothy Are you talking about the name as it will appear in the history? Then have a look at the following wiki page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_... Regards, Hans On 10/12/2011 10:50 AM, Timothy Wu wrote:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Wed, Oct 12, 2011 at 5:23 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Timothy
Are you talking about the name as it will appear in the history?
Then have a look at the following wiki page:
http://wiki.g2.bx.psu.edu/**Admin/Tools/Tool%20Config%** 20Syntax#A.3Coutputs.3E_tag_**set<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set>
Regards, Hans
Hi Hans, Yes I think so. Is there a way to do that if I have variable number of output that would not be known until the run time? Timothy
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 [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Timothy Wu [2huggie@gmail.com] Sent: Wednesday, October 12, 2011 4:51 AM To: 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
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> 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 [ galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Timothy Wu [ 2huggie@gmail.com] Sent: Wednesday, October 12, 2011 4:51 AM To: 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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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;
participants (4)
-
Hans-Rudolf Hotz -
Paniagua, Eric -
Ross -
Timothy Wu