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
Minor changes to conf file and readme
README to reStructuredText

first modification to changing README to rst format. Considering
splitting the file up when placing into the docs/book
minor formatting change
format
Rebased off of master branch 1.1

rebased off of master branch and split the README into:
book\src\introduction\tools_what.rst
book\src\usage\tools_results.rst
book\src\usage\tools_submit.rst

Future Work: merging the tools_*.rst files into the respective .rst
files within the directory's they are placed in.