Invoking the tool
The previous step specified the environment needed for the tool to work. However, it did not specify what actions need to be taken to actually run it. This is where the "tool script" comes in: it tells the platform how to actually run the tool with a given set of input parameters to create a set of output files.
You can put your script in the box on the left. This might be a one-line function call with the parameters as arguments, or a longer script where the parameters are used to set variables. You can choose the programming language the script is written in using the dropdown menu at the top.
When you run code on a local machine, you don’t need to specify outputs because all outputs are created within your local file system. With Ontologic, code is running inside a container that has an independent file system. We copy output files out of the container at the end of a run before shutting it down. By default, only files that are in a top-level "outputs" directory will be saved when the tool runs.
For example, if you are saving your results to a csv file, you'll need to make sure it gets saved to the following location: