[galaxy-dev] Galaxy workflow with variable inputs

I'm curious if there is a way to create a workflow as follows (or if anyone else thinks this is a good idea, or for that matter has a good suggestion of another solution):

1) User selects N groomed fastq files and puts them in a history

2) User selects a workflow that allows them to select the N files, and then passes each of them to a two step process that first runs them through tophat, and the resulting bam file through cufflinks.

3) At the other end of the workflow would be a merge module that would take one of the 3 output files from cufflinks from each run, and does some sort of aggregation or transformation step on all the resulting data.

Any input would be greatly appreciated.

Thanks,

Dave