TOPPAS allows you to create, edit, open, save, and run TOPP workflows. Pipelines can be created conveniently in a 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 -in <file>.

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

To create a new TOPPAS file, you can either:

• open TOPPAS without providing any existing workflow - an empty workflow will be opened automatically
• in a running TOPPAS program choose: File > New
• create an empty file in your file browser (explorer) with the suffix .toppas and double-click it (on Windows systems all .toppas files are associated with TOPPAS automatically during installation of OpenMS, on Linux and MacOS you might need to manually associate the extension)