Like most days, JJ very politely pointed out that I am a wrong this morning. You can have variable numbers of outputs at runtime, see the last section ("Number of Output datasets cannot be determined until tool run" ) of this page: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files Sorry about that. -John On Tue, Oct 16, 2012 at 8:48 AM, John Chilton <chil0060@umn.edu> wrote:
I don't believe this is possible in Galaxy right now. Are the outputs independent or is information from all inputs used to produce all outputs? If they are independent, you can create a workflow containing just your tool with 1 input and 1 output and use the batch workflow mode to run it on multiple files and get multiple outputs. This is not a beautiful solution but it gets the job done in some cases.
Another thing to look at might be the discussion we are having on the thread "pass more information on a dataset merge". We have a fork (its all work from Jorrit Boekel) of galaxy that creates composite datatypes for each explicitly defined type that can hold collections of a single type.
https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes...
This would hopefully let you declare that you can accept a collection of whatever your input type is and produce a collection of whatever your output is. Lots of downsides to this approach - not fully implemented, and not included in Galaxy proper, your outputs would be wrapped up in a composite datatype so they wouldn't be easily processable by downstream tools. It would be good to have additional people hacking on it though :)
-John
------------------------------------------------ John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 Bitbucket: https://bitbucket.org/jmchilton Github: https://github.com/jmchilton Web: http://jmchilton.net
On Tue, Oct 16, 2012 at 7:13 AM, Sascha Kastens <s.kastens@gatc-biotech.com> wrote:
Hi all!
I have a tool which takes one ore more input files. For each input file one output is created,
i.e. 1 input file -> 1 output file, 2 input files -> 2 output files, etc.
What is the best way to handle this? I used the directions for handlin multiple output files where
the ’Number of Output datasets cannot be determined until tool run’ which in my opinion is a bit
inappropriate. BTW: The input files are added via the <repeat>-Tag, so maybe there is a similar
thing for outputs?
Thanks in advance!
Cheers,
Sascha
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