I'd suggest:

1) Make your new datatype a subclass of Html - it's a subclass of composite that contains an HTML document as the object's native display - so it can inform users what's there.

2) When constructing these new things, pass the file_path of the Html (composite) dataset subclass to your wrapper on the command line

3) Your wrapper code can construct any arbitrary structure as long as it's rooted in that directory - Galaxy stores it without any fuss. The wrapper should also populate the Html file itself with nicely

laid annotation for the user to check out.

4) The key is that all tools that take this new datatype as input must know how to decode this structure - they must be passed the $input.extra_files_path which gives them that same path root.

5) Yes, it's odd and annoying that it's extra_files_path for files_path. Go figure.

6) grep extra_files tools/*.xml to find some examples - I think the velvetg one uses a complex subdirectory structure - but it doesn't really matter - as long as your tools know how to deal with it, it's just a directory to Galaxy!

I hope all this helps...

On Wed, Jan 30, 2013 at 8:22 PM, Pierre Pericard <pierre.pericard@sb-roscoff.fr> wrote:

In that case, could anyone point me to an example of a Composite Datatype which could accept as input an unknown number of files in an unknown number of directories. I can't seem to understand how that would work based on the wiki.

But maybe are we anticipating a near functionality of Galaxy. There were talks about changing the way Galaxy handle zip files, is it still on the table ?

Thank in advance for any help,

Pierre

Pierre Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/

Le 29/01/2013 18:04, Peter Cock a écrit :

On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
<pierre.pericard@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.

Peter

___________________________________________________________