Re: [galaxy-dev] Tool wrapper XSD

2013-02-22 Thread Jean-Frédéric Berthelot
 Is there a Galaxy XML tool wrapper XSD ?

 https://github.com/JeanFred/Galaxy-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

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Re: [galaxy-dev] Tool wrapper XSD

2013-02-20 Thread Pierre Pericard
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/galaxy.xsd

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.peric...@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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Re: [galaxy-dev] Tool wrapper XSD

2013-02-20 Thread Jean-Frédéric Berthelot
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

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Re: [galaxy-dev] Tool wrapper XSD

2013-02-19 Thread James Taylor
On Tue, Feb 19, 2013 at 3:39 AM, Pierre Pericard
pierre.peric...@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
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Re: [galaxy-dev] Tool wrapper XSD

2013-02-19 Thread John Chilton
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/galaxy.xsd

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.peric...@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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