Fix bug preventing tool wrappers from be written to the new tool_files directory.
Fix bug preventing tool wrappers from be written to the new tool_files directory.

jmchilton/lwr,galaxyproject/pulsar,jmchilton/pulsar,jmchilton/pulsar,ssorgatem/pulsar,natefoo/pulsar,natefoo/pulsar,jmchilton/lwr,ssorgatem/pulsar,galaxyproject/pulsar