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.

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