Provide Parameter Documentation

There is no description or link to a description of parameters on the site. Even looking at 

https://github.com/PathwayAndDataAnalysis/causalpath/blob/master/wiki/InputFormat.md

has problems. causalpath.org parameters such as: "Transcription factory activity inference file" are hard to map to InputFormat.md. There is no mention of the word "factory" on the InputFormat.md

