matlab + galaxy

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matlab + galaxy

do kadya
Hi,
How can I call Matlab command in Galaxy ?
I refer this link, but don't know how to use it. 


I am learning Galaxy, hence don't know much about it.

Can i write that command in xml file to integrate it as tool ?

I am using below website to create xml files for Matlab. Is it good website to create xml files ?

Waiting for positive reply.

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Re: matlab + galaxy

Björn Grüning-2
Hi,

I think you should start here:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Furthermore, Peters Blast wrappers are always a good start to learn writing Galaxy Tools.
https://github.com/peterjc/galaxy_blast

Here you can find a variety of small to complex wrappers:
https://github.com/bgruening/galaxytools

All of them should be a good start to integrate your matlab script. But the first step would be to make your script commandline accessible. If its possible consider to use octave as alternative. In that way you can share you wrapper with everyone, also with peoples that do not have a matlab license.

Cheers,
Bjoern


Hi,
How can I call Matlab command in Galaxy ?
I refer this link, but don't know how to use it. 


I am learning Galaxy, hence don't know much about it.

Can i write that command in xml file to integrate it as tool ?

I am using below website to create xml files for Matlab. Is it good website to create xml files ?

Waiting for positive reply.


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/