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.Laros@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.Laros@lumc.nl