The Center for Phage Technology's Galaxy tools.
The repository quality is currently all over the place, so please don't use this as examples of good practice or anything :) Eventually all of these tools will be folded into one of the other large repositories for continued maintenance, such as Björn's galaxytools or the IUC repo
NONE of these tools are written/configured for the Toolshed. They will be eventually, but that's a wishlist item.
Except where otherwise noted, all code is GPLv3.