The general case is hard and it was brought up repeatedly at the
Galaxy community conference. One path might be this work
(https://bitbucket.org/galaxyp/galaxy-central-homogeneous-composite-datatypes)
on defining datasets that represent homongenous collections of files,
but there are no easy answers currently.

As for the comment about paired-end sequence workflows, such workflows
should actually be doable now in Galaxy (since pull request 75). All
you need to do is comment out line 40 of templates/workflow/run.mako
and then you should be good to go.

-John

On Sat, Nov 10, 2012 at 4:04 PM, Anthonius deBoer <thondeb...@me.com> wrote:
> Very likely you have to use the API for these kinds of workflows.
> The UI for Galaxy is very limited in workflows that deviate from the One
> Input paradigm.
>
> Even for the most common workflow (paired end DNA sequencing of multiple
> samples ) you have to resort to using the API...Puzzling...
>
> Regards,
>
> Thon de Boer, Ph.D.
> Bioinformatics Guru
> +1-650-799-6839
> thondeb...@me.com
> LinkedIn Profile
>
>
>
>
> On Nov 8, 2012, at 5:13 AM, LUO Yufei <yufei....@versailles.inra.fr> wrote:
>
> Hello,
>
> The number of inputs is not fixed for my workflow, maybe I have 6 inputs,
> maybe more than that, the number of inputs depends on what data I have for
> the analysis.
> As I know, in a workflow, all inputs should be pre-defined...that is to say,
> the number of inputs is known before running one workflow.
> Do you have any idea for this problem? How can I do to make a workflow with
> the variable number of inputs?
>
> In advance, thanks for the answer,
> Yufei
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