Added files and changes for analysis package 'tool'

The tool package allows a user to specify a tool to be run on a sample.
Ability to pass options to both the tool and sample is included as well
as the ability to use tools that require multiple files.
Syntax Error

Fixed syntax error and also changed check() function in tool.py to work
even if the process finished before check was ran.
minor correction
Add Documentation
Clean up `check` function in tool analysis package.
A bit of cleanup
Changes to allow --tool_dir to be independant
Several quality changes

Changed it so that the output of the tool is returned in the file
"tool_output.log"
The command that is run is written to "analysis.log"
Instead of using `sample` to indicate the sample in the command, now
'$sample` must be used.
Shell = True  ---> Shell = False
self.tool_pid  ---> self.tool_process
Changes to allow --tool_dir to be independent
Merge remote-tracking branch 'development/development' into tools
Minor changes to conf file and readme
Merge branch 'tools' into development

Conflicts:
	utils/submit.py