Brian,

> For the
> initial trinity de novo assembly, I took Jeremy's initial workflow and
> tweaked it to work with the latest release - and submitted it to the
> galaxy tool shed.  

Excellent. I'll remove my old Trinity wrapper from our code base and point 
people to your wrapper.

> There are some complexities here, such as not knowing ahead of time
> how many different samples are to be processed - so this needs to be
> determined dynamically, which impacts the overall complexity of the
> total workflow.  Is this possible in Galaxy, and if so, are there
> examples I can work from?

Take a look at the repeat element; it enables a user to specify a number of 
inputs to a tool.

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crepeat.3E_tag_set

Tool wrapper that use the repeat element include the GATK's depth of coverage 
and Cuffdiff.

Best,
J.
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