Hello Julie,

  Right now Galaxy can implicitly create collections by running a tool
that takes in a single input or a paired dataset over say a list of
inputs or a list of paired inputs but tools cannot explicitly create
dataset collections. I think Galaxy's current capabilities add a lot
of useful functionality - but say tools that take a big input and
split it into an arbitrary number of pieces or tools that
normalize/summarize N inputs simultaneously and produce N outputs
cannot be represented. A few people made some progress on this at the
recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more
people have made it clear that it is an important feature.

Sorry.

-John

On Mon, Jul 28, 2014 at 11:47 AM, julie dubois <dubjulie@gmail.com> wrote:
> Hi all,
> I'm working with data_collection as type of input in xml files. but I
> use all the datasets of a collection to compute some results that I
> want to push in a "data_collection" output.
> I know how take each dataset of a data_collection input with my
> script, like this :
> <configfile name="shscript">
> ...
> for $f in $input
> ...
> </configfile>
> where $input is defined by <param name=$input1 type=data_collection
> collection_type=list... in the top of my xml file.
>
> But if my script produce some outputs (number of outputs not defined
> in advance), how can I populate an output as a data_collection with my
> shscript and how should I define this output in the xml ?
>
> Thanks
> Julie
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