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:

You can play with existing example pipelines, which cover identification, quantification and some special use cases, such as SubsetNeighborSearch. To open an existing example pipeline, select File > Open example file from the menu bar in TOPPAS. See Examples below for details.

To create a new (empty) 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 with the suffix .toppas

All .toppas files are usually associated with TOPPAS automatically during installation of OpenMS - at least on Windows. On Linux and MacOS you might need to manually associate the .toppas extension.