e.g. Tar-ball contains temp files from common Unix editors:

$ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/nlstradamus/ && tar -xvf shed_upload.tar.gz
cp '/tmp/tmpDhxzFT' 'shed_upload.tar.gz'
#README.rst#
README.rst~
README.rst
nlstradamus.xml
tool_dependencies.xml

Either planemo needs some additional default excludes, or perhaps it could read the local .gitignore to expand the exclude list? (I would have said that was too magic, but planemo seems to do a lot of clever stuff like this already)