pm_uep_opt fails when den_fmt has custom name

[patrick-austin]

The tool wrapper is replacing (but not setting) chden_path and chden_seed in the param file to match the galaxy dataset name. If these aren't present (they're not, as the config generator never sets them) then it will default to the seedname of the structure which means the workflow will fail unless you happened to name the file the same thing.

In other places we have logic required to do the "replace or set" using sed, so copy that and add tests to cover this case.

EDIT: Actually the issue is that the wrapper implicitly assumes that the dataset name will end with a file extension, e.g. seed.den_fmt or even seed.txt, and will try to remove this from the end (to define a seed name seed), then add it back and load (seed.den_fmt). This fails when .den_fmt is not in the name, as then the file on disk has just the seed (removing the non-existent extension has no effect), but we try and load seed.den_fmt