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 jochen.bick@usys.ethz.ch 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/

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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 » <galaxy-dev-bounces@lists.galaxyproject.org au nom de jochen.bick@usys.ethz.ch> 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/

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