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 Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX

Le 29/01/2013 18:04, Peter Cock a écrit :
On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
<> 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
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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