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/compare 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.kast...@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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
