Dear Peter,

On Fri, May 13, 2011 at 02:41:26PM +0100, Peter Cock 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?

Well, none to be honest. But if I'm going to add a substantial amount of tools
I'd rather define the interface than write wrappers. An additional advantage is
that I can reuse the interface description for other purposes.

> 
> 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.

Okay, thank you for your feedback.


With kind regards,
Jeroen.

> 
> Peter

-- 
Jeroen F. J. Laros - j.f.j.la...@lumc.nl
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