Hi everyone, Is there a Galaxy XML tool wrapper XSD ? Thanks, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/
On Tue, Feb 19, 2013 at 3:39 AM, Pierre Pericard <pierre.pericard@sb-roscoff.fr> wrote:
Is there a Galaxy XML tool wrapper XSD ?
No, but if anyone would like to make such a schema we would be happy to include it. -- James Taylor, Assistant Professor, Biology/CS, Emory University
Hey Pierre, If you are going to write one and want a starting point, here is the schema I used for incorporating Galaxy tools into a Java web service workflow framework called TINT: https://github.com/jmchilton/TINT/blob/master/projects/TropixGalaxy/schema/g... It is mostly a subset of actual valid tools (even more so because of how dated this has become), but it has some extensions for storing literal test results right in the test XML and literal configfiles (i.e. non-cheetah) that you will probably want to rip out. -John On Tue, Feb 19, 2013 at 2:39 AM, Pierre Pericard <pierre.pericard@sb-roscoff.fr> wrote:
Hi everyone,
Is there a Galaxy XML tool wrapper XSD ?
Thanks, Pierre
-- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/
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Ok, thanks a lot. I'm not sure I will have the time to develop a XSD but after looking at yours I think it would only need a few contributors to get a fully complete and updated one. Thanks again, Pierre Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/ Le 19/02/2013 15:13, John Chilton a écrit :
Hey Pierre,
If you are going to write one and want a starting point, here is the schema I used for incorporating Galaxy tools into a Java web service workflow framework called TINT:
https://github.com/jmchilton/TINT/blob/master/projects/TropixGalaxy/schema/g...
It is mostly a subset of actual valid tools (even more so because of how dated this has become), but it has some extensions for storing literal test results right in the test XML and literal configfiles (i.e. non-cheetah) that you will probably want to rip out.
-John
On Tue, Feb 19, 2013 at 2:39 AM, Pierre Pericard <pierre.pericard@sb-roscoff.fr> wrote:
Hi everyone,
Is there a Galaxy XML tool wrapper XSD ?
Thanks, Pierre
-- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/
___________________________________________________________ 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,
If you are going to write one and want a starting point, here is the schema I used
Thanks John for sharing your XSD. I forked and started to complete it at: <https://github.com/JeanFred/Galaxy-XSD> I worked on it until my own tool wrapper passed, but it needs more work for any other wrapper I tested. Many wrappers also use constructs which are not yet documented on the ToolConfigSyntax wiki page (like 'compare' attribute on output tests for example), so I was unsure to incorporate those. Hope that helps, -- Jean-Frédéric Bonsai Bioinformatics group, LIFL
Is there a Galaxy XML tool wrapper XSD ?
I worked more on this XSD. It now passes 181 (and fails on 163) of the 352 tools packaged in galaxy-dist − it starts being somehow useful.
Many wrappers also use constructs which are not yet documented on the ToolConfigSyntax wiki page.
I dug into Galaxy source code to make sure these undocumented structures actually made sense somewhere. When I could find where it was used, I added it to the XSD with an <!-- undocumented --> comment. Hope that helps, -- Jean-Frédéric Bonsai Bioinformatics group, LIFL
participants (5)
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James Taylor -
Jean-Frédéric Berthelot -
Jean-Frédéric Berthelot -
John Chilton -
Pierre Pericard