I've been spending a bit of time looking over Data Sources for Galaxy.  I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Galaxy, along with some user credentials.  In this sense it would be similar to the GenomeSpace importer tool.

However, instead of just exporting a set of files to a user's history, I'd like to be able to also automatically group these files into a dataset collection.  I would also like to be able to link to these files instead of creating copies (which I think I can only do through a Data Library am I correct?).  Ideally, I'd like to be able to use this tool as the first step in a workflow, which would allow me to import and structure the data needed for the rest of the workflow.