Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

It is for when the dependency was installed into galaxy but where planemo is not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps.
Christian
University of Manchester