Would require some adjustment on the server side of the webtool I think: to allow getting data in from URLs and to export the results to a URL (API).

On the wiki, you can find this info on how to get data IN into Galaxy: http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources

But there is no way to get data out of Galaxy to your webtool I think, and get the results back in a way that Galaxy knows what has been executed. (Perhaps one possible start of a solution: make your dataset public, and send the URL (if on a public Galaxy) to the tool (if it accepts URLs)).

Anyway, on a higher level, the purpose of Galaxy is not to communicate with webtools, but providing a front-end to command-line tools and a data tracking and analysis platform. (all of which collides with the integration of webtools IMO) (also like: sometimes you don't even get the source-code behind a scientific webservice).

Have a nice wednesday,

Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 11/07/2012 12:34 AM, Franco Caramia wrote:
Yes, primer3 is available as a command line tool, it was just an example,
the one I'm actually after is optimus primer..
I'm sure there are several web-tools out there that would be nice to get to
Galaxy...
Any Ideas??

Regards,

Franco


On 5/11/12 11:18 PM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote:

On Mon, Nov 5, 2012 at 5:53 AM, Franco Caramia
<franco.cara...@petermac.org> wrote:
Hi list,

I¹m trying to find documentation or examples on how to wrap web-tools
(like primer3, optimus primer) in Galaxy.

Any useful links or examples would be of great help.

Thanks,

Franco
I'm not answering your question, but Primer3 is available as a command
line tool, so why do you want to wrap a web-tool version of it?

Also EMBOSS have a command line wrapper providing a conventional
Unix API to primer3. There are some EMBOSS wrappers in the Galaxy
ToolShed, but I don't see one for primer3 yet.

Regards,

Peter

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