use or convert tool.xml file for database webpage

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use or convert tool.xml file for database webpage

Jochen
Hi,

I have a question regarding the layout of each tool. I would like to use
the same layout (same xml file) like inside galaxy to build a standalone
webpage for a database. Is it possible to convert or use the xml file
outside galaxy? My problem is that I have no idea how the xml file get
interpreted inside galaxy to generate the interface of a galaxy tool.

thanks in advance Jochen
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Re: use or convert tool.xml file for database webpage

Peter Cock
Hi Jochen,

I think you will find this very difficult without including a large
chunk of the Galaxy code in your project for turning a tool
XML file into an object representation.

Although the main features of the tool XML provide a quite
neutral tool description (list of arguments, output filenames,
and a template to build the command line), there are a lot
of complications and rarely used bits which make doing
this in general very hard.

Galaxy has at least two sections of the code which interpret
the tool file XML to present a user-interface. First, there is
the main interface for running a tool. Second, there is a tool
preview in the Tool Shed - but that does not fully understand
the tool XML and is much more limited.

Could you not provide a limited Galaxy instance instead?
Just your tool and any other key functionality needed to
use with it (importing files perhaps, maybe some plotting
or filtering commands)?

Peter


On Tue, Feb 6, 2018 at 9:34 AM, Jochen Bick <[hidden email]> wrote:

> Hi,
>
> I have a question regarding the layout of each tool. I would like to use
> the same layout (same xml file) like inside galaxy to build a standalone
> webpage for a database. Is it possible to convert or use the xml file
> outside galaxy? My problem is that I have no idea how the xml file get
> interpreted inside galaxy to generate the interface of a galaxy tool.
>
> thanks in advance Jochen
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
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Re: use or convert tool.xml file for database webpage

Jochen
Hi Peter,

thanks for your quick reply.

>
> Could you not provide a limited Galaxy instance instead?
> Just your tool and any other key functionality needed to
> use with it (importing files perhaps, maybe some plotting
> or filtering commands)?

hmm the problem is that I would like to use this for a publication and
also provide a galaxy tool which will then access the database webpage.
Right now I just have a tool that access the mysql database in our local
galaxy instance.
I guess a webpage would be nicer for non galaxy user.

Cheers Jochen
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Re: use or convert tool.xml file for database webpage

Gildas Le Corguillé
Hi Jochen,

Note that there are some projects which propose a layer, a web interface, over the Galaxy engine.
Those solutions are using the API (BioBlend) to display Galaxy objects from the history, and to launch jobs.

Here is two of them:
MetaGenSense: https://f1000research.com/articles/4-86/v3
https://ngphylogeny.fr


Cheers

Gildas

Le 06/02/2018 11:07, « galaxy-dev au nom de Jochen Bick » <[hidden email] au nom de [hidden email]> a écrit :

    Hi Peter,
   
    thanks for your quick reply.
   
    >
    > Could you not provide a limited Galaxy instance instead?
    > Just your tool and any other key functionality needed to
    > use with it (importing files perhaps, maybe some plotting
    > or filtering commands)?
   
    hmm the problem is that I would like to use this for a publication and
    also provide a galaxy tool which will then access the database webpage.
    Right now I just have a tool that access the mysql database in our local
    galaxy instance.
    I guess a webpage would be nicer for non galaxy user.
   
    Cheers Jochen
    ___________________________________________________________
    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:
      https://lists.galaxyproject.org/
   
    To search Galaxy mailing lists use the unified search at:
      http://galaxyproject.org/search/


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