Clean up quickmodel

[sonyahanson]

• Move 95% interval plotting to plots.py
• Add ability to increase samples through inputs.py
• Add ability to use filesets for single wavelength assays.
• Include subset of data used for analysis in output file
• Include recently added things in output file (equilibration, 95% interval)

Longterm:

• Add autoprotocol analysis via quickmodel

[sonyahanson]

Look at that, without even looking at this issue, I've solved most of these issues in #97 .
Other things still on the list:

• more flexible layout #91
• add trace option #87
• fix hacky json / inputs.py setup
• Add option to Plot two datasets to compare (a la 'constph-grant' or 'GK v. WT' requests)
• Make it a bit clear what the default nsamples is