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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/