For example:

Could be: A sequence of tools run on input data such as an mzML file which produces an output. There are over 185 TOPP tools to choose from.

Could be: TOPP is an application built using OpenMS. TOPP consists of many tools.

Could be: TOPPAS is an application which provides a GUI to create, edit and apply TOPP tools. TOPPAS is no longer supported and has been replaced by KNIME.