We can hack the old wrapper back in, using a hard-coded path to the old cuffdiff.
You could also use Managed Tool Dependencies for multiple versions of cuffdiff:
Shantanu suggests it might be a better world if we create a tool-shed repository for the cuffdiff 1.3-2.1 (wrapper 0.0.5) version, then install that.
Would that be a better path, or just add confusion?
This is on the right path. The right thing to do is migrate the Cuff* tool wrappers out of the galaxy-central/dist repositories; this is a bit more effort than simply creating the tool-shed repository for the wrappers.
There are two reasons I haven't done this:
(a) time;
(b) because the tools—and consequently the wrappers—are still in active development, there needs to be a place for managing development of the wrappers. Hence, the wrappers need a home on bitbucket or github, but we (the Galaxy team) haven't determined where these wrappers should live.
(a) is a much more significant barrier than (b), so if a pull request migrating Cuff* tools out of the distribution were made, I'm sure (b) could be worked out.
Best,
J.