In a former position I wrote extensions to Galaxy that allow workflows
such this:

https://bitbucket.org/galaxy/galaxy-central/pull-request/116/multiple-file-datasets-implementation/diff
https://bitbucket.org/msiappdev/galaxy-extras/commits/all
http://bit.ly/beyond-proteomics

so believe me I understand this is important. I was recently hired by
the Galaxy team and am now working on a more palatable variant on
these ideas. More palatable also means  more complex and more work to
implement unfortunately... but I am working on it.

In the meantime, have you considered driving these kind of workflows
via the API? I think the refinery platform
(https://github.com/parklab/refinery-platform) for instance targets
the Galaxy API and rewrites workflows at runtime to handle variable
numbers of inputs mitigating Galaxy's limitations. This would require
some custom development and some mechanism outside of the traditional
Galaxy channels to launch the workflows and probably is not worth the
effort unless you are talking about a small pool of fixed workflows.

-John

On Tue, Dec 10, 2013 at 4:05 AM, Preussner, Jens
<jens.preuss...@mpi-bn.mpg.de> wrote:
> Dear galaxy-dev’s,
>
>
>
> about a year ago you discussed on variable number of inputs into a workflow
> (see http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-November/012012.html
> and
> http://thread.gmane.org/gmane.science.biology.galaxy.devel/4502/focus=4502,
> for example). We’re interested in having something simple like a number of
> fastq files that have to undergo automated quality control and trimming. A
> workflow would describe steps that need to be done per file (like fastqc,
> quality trimmer and so on), and in the end, a tabular data summarizes
> statistics on all files. Of course, we could prebuild workflows for
> 2,3,4,5,..n input files and join the output, but it would be much cooler to
> have it variable. Since it’s possible to start many instances of a workflow
> (i.e. one instance per file), this would be a good starting point. But how
> would one combine outputs of those instances? Is anyone out there having
> experience with such setups? Which files are involved in starting many
> instances of a workflow? Any other ideas or suggestions on how to go from
> here? Thanks a lot for any input!
>
>
>
> Best,
>
> Jens
>
>
>
> Max-Planck-Institute for Heart and Lung Research
>
> Bioinformatics Service - FGI
>
> Ludwigstraße 43
>
> 61231 Bad Nauheim
>
>
>
> Phone. +49 6032 705 1765
>
> Mail. jens.preuss...@mpi-bn.mpg.de
>
>
>
>
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