Add comments to the generated R scripts

[Treutler]

This would make the code appear more structured and easier to understand.

Suggestion: subdivide the code into sections:

• import DiffLogo functions [should be library(DiffLogo) some day!]
• input folder and output folder (to be adapted!)
• parse and check input files
• configure and create motif comparison
• create visualization and write output file(s)