Hi Timothy, On Tuesday, September 20, 2011, Timothy Wu <2hug...@gmail.com> wrote: > Hi, > > Looking under the tools directory I realized that some tools > comes with *_wrapper.py. I wonder under what circumstances > is this needed?
Mostly messing about with stderr (there is a long standing bug open about this handling this in Galaxy itself) or with filenames (moving/renaming outout, sometimes copying/ linking input) for annoying tools which insist on fixed names or extensions. > I'm trying to do a quickie for RepeatMasker. It looks to > me like the tool does not allow one to specify the name > of the output files. It also appears to me that tools should > have an $output variable specifies within the <command> > tag. So I was wondering if this is one case where a > wrapper.py is needed. Yes. Unless the tool can write it's output to stout, In which case the <command> can use that to capture stout to the filename Galaxy selects for the output file. 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/
