Hi Jeroen,

The idea of having a tool to automatically generate Galaxy wrappers is attractive, and in some cases, possible. For example, I know that the tools in QIIME (http://qiime.sourceforge.net/) use some sort of argument declaration and a Python module to read it and deal with the command-line interface. This makes it possible to write a converter that would generate (or at least kickstart) Galaxy wrappers. I also have some Perl scripts that use the Getopt::Euclid module (http://search.cpan.org/dist/Getopt-Euclid/), which declares all the arguments taken by the program. I have been contemplating writing code that would convert the Getopt::Euclid specifications into a Galaxy wrapper.

At the moment, though, there are quite a few outstanding irritating bugs in the Galaxy wrapper system that force you to use workarounds to get a working wrapper: https://bitbucket.org/galaxy/galaxy-central/issues?component=tools-config&sort=id <https://bitbucket.org/galaxy/galaxy-central/issues?component=tools-config&sort=id>. Needless to say that it would be easier to automated wrapper generation if these bugs were fixed.

Regards,

Florent




On 14/05/11 00:03, J. F. J. Laros wrote:
Dear Dave,

This indeed sounds like an interesting alternative. I'll look into it.


With kind regards,
Jeroen.

On Fri, May 13, 2011 at 01:48:12PM +0000, Dave Walton wrote:
An alternative might be to have something like GenePattern has.  It's not as
seamless for the person who wants the wrapper as what's been suggested here,
but it's easier than creating a lengthy XML file.

GenePattern has an HTML Form interface for entering all the components of
your tool, including the command-line you want to expose and the parameters
you want to make available, and then it generates the back-end.

There are definite down-sides to this.  I've never tested what keeps the
tool in GenePattern from letting you do destructive things.

Dave


On 5/13/11 9:41 AM, "Peter Cock"<p.j.a.c...@googlemail.com>  wrote:

On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros<j.f.j.la...@lumc.nl>  wrote:
Hi Pieter,

Thanks for the reply, but from the looks of it, this is a way to incorporate
webservice clients into galaxy. What I want is slightly different.

I'm talking about adding a normal command line tool (an aligner for example)
but I'm not willing to write a wrapper each time (the wrapper for BWA for
example is 327 lines). If a computer readable description of the interface
exists, this description can be used to generate a python wrapper. I
mentioned
WSDL because this also gives a description of an interface, but any
equivalent
description would of course be fine.

Ideally, such a description is maintained by the developer of the tool in
question.

With kind regards,
Jeroen.
How many tools can you name that come with such a machine readable
file describing their command line interface?

I can think of only one - the EMBOSS tool suite and their ACD files
(used internally by EMBOSS to generate the command line help,
documentation, and do the command line option parsing).

Unfortunately I don't think there is an easy answer - even if wrapping
a tool where all the input and output formats are already supported in
Galaxy.

Peter
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