wrappers are also used when a tool produces several files in an output folder (i.e. executable takes outdir parameter, not explicitly named outfile paths) and you would like to move these to the desired paths under files/ (i.e. a composite datatype is not desired) and/or cleanup unnecessary files.

On Mon, Sep 19, 2011 at 11:41 PM, Peter Cock p.j.a.cock@googlemail.comwrote:

Hi Timothy,

On Tuesday, September 20, 2011, Timothy Wu 2huggie@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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