4.2 years ago by
Martin's advice to explore using data libraries for shared data is a good one. You can also put in comments on your tool form about where to find sample/default data (which library, etc.). Being able to select files from Shared Libs on the tool form directly - without needing to import the data into a history first, is an idea we have been thinking about. Not implemented as far as I know (Marten can add more about this).
Now, reference genomes can be incorporated into a tool form directly no problem. Check out the wrapper for a mapping tool like BWA to see how (although many many tools incorporate this option). You can sort this list of genomes in the pull-down any way you want sort of the associated loc file == sort in the display). So if one was the "default" - then sort so it is first and maybe put a comment on the tool form near the selection/parameter name.
Hope this helps, Jen, Galaxy team