I'm sorry for the late response to this - I don't have any great advice regarding debugging these tool_dependencies.xml issues. I think those virtualenv tags are particularly brittle and I recommend switching to a more manual approach to Python dependencies if you are going to continue using tool_dependencies.xml - setting up packages for each Python package and referencing them the way say Macs2 does https://github.com/galaxyproject/tools-iuc/blob/master/tools/macs2/tool_dependencies.xml
That said - the IUC and devteam have stopped writing tool_dependencies.xml files and have switch to Conda for all of our packaging. There is some documentation here:
Conda dependencies should be a bit more transparent - at least during this development stage.