Changed the intermediary script parse the command line args. It will all args before the 'start' keyword, and pass all args after to the tool being executed. The only command line args it currently uses are used to specify that the input file will be used as the output file, and to specify what the output file is.
The changes to the intermediary script seem to work for spice init.
The new version of the intermediary script 'isisToolExecutor.py' failed to correctly handle cases where no args for the intermediary script were given. This is because it incorrectly identified the isis tool name as improperly formatted arg. The script now checks for the existence of the separating keyword before trying to parse the command line arguments. With this new version I was able to successfully run spiceinit->ctxcal->ctxevenodd where ctxcal and ctxevenodd had no intermediary script args.
Merge pull request #5 from codythompson/betterIntermediaryScript

Better intermediary script
Small fix to temp install script
Added wrapper for mroctx2isis that uses intermediary script
Updated xmlTranslator to stip whitespace on text.
Merge https://github.com/codythompson/capstone_repo into Tools_With_Params

Conflicts:
	galaxy/tool_conf.xml

fixing my local repo
xmlTranslator removes extra spaces in text, still need to parse and discover necessary datatypes.
xmlTranslator should handle most basic files.  No params yet.
Merge branch 'Tools_With_Params' of https://github.com/codythompson/capstone_repo into Tools_With_Params