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