On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
<pierre.peric...@sb-roscoff.fr> wrote:
> If I'm not mistaking, Composite Datatypes allow for only one directory,
> whereas we need to keep a constant directory structure with 2 or more
> sub-directories containing our input files.

I'm not sure if that is true - the example of HTML output with images
comes to mind as a common use-case where subfolder(s) would be
expected. I've only had limited first hand experience with Galaxy's
composite datatypes myself though.

> We have no way to change these tools behavior (obviously not Galaxy-friendly
> ;-) ) and therefore need to maintain this structure in the job working
> directory.

Perhaps a tool wrapper could create a dummy folder using symlinks
(faster and less wasted disk than copying files), but that isn't ideal.

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