TOPPAS allows you to create, edit, open, save, and run TOPP workflows. Pipelines can be created conveniently in the TOPPAS GUI. The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition in the .toppas file. Furthermore, TOPPAS interactively performs validity checks during the pipeline editing process and before execution (i.e., a dry run of the entire pipeline), in order to prevent the creation of invalid workflows. Once set up and saved, a workflow can also be run without the GUI using ExecutePipeline.

The following figure shows a simple example pipeline that has just been created and executed successfully:

Note: Some example pipelines are shipped with OpenMS and can be opened in TOPPAS by selecting File > Open example file. Also see Examples for more information.