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
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