> I recommend to use the repeat tag (see 
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the 
> existing parameter to make it possible to select multiple files.

Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of 
how to use this tag.

Gus, if you end up modifying the Tophat wrapper to support multiple input 
datasets, please submit a patch or fork galaxy-central via bitbucket and I'll 
integrate these enhancements into the Galaxy code base as this would be nice 
functionality to have.

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