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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