This script gives you the version of the used tools and their reference. The command line for getting the version and the reference information are stored in a separate configuration file in a form of tab sep file:
tool_id command line reference paper
Example:
fastqc fastqc --version "Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc"