PEP-8 fixes and comments for workflow_util.py.
Remove unused method.
Rearrange module arguments to bring ts workflow modules more inline with Galaxy.
Will enable remove tool shed specific input module in a subsequent changeset.
Remove unused methods.
Rework tool shed's workflow module factory so only tool module needs to be different.
Fixes dataset collection inputs in the tool shed. Furthermore, this will allow all all future non-tool modules to be the same between Galaxy and the Tool Shed as well. May seem hacky - but it is removing duplication and it makes some intuitive sense that only the tool module would need to function differently between Galaxy and the tool shed anyway - input parameters, if statements, stop and review steps, etc... will all likely not depend on tool shed artifacts.
Make run_tool_shed.sh executable.