Adding workflow tests with Planemo

1. Find a tutorial that you’re interested in, that doesn’t currently have tests.

   This tutorial has a workflow (.ga) and a test, notice the -test.yml that has the same name as the workflow .ga file.

   machinelearning/workflows/machine_learning.ga
   machinelearning/workflows/machine_learning-test.yml
   

   You want to find tutorials without the -test.yml file. The workflow file might also be missing.

2. Check if it has a workflow (if it does, skip to step 5.)
3. Follow the tutorial
4. Extract a workflow from the history
5. Run that workflow in a new history to test

6. Obtain the workflow invocation ID, and your API key (User → Preferences → Manage API Key)

   

7. Install the latest version of planemo

   # In a virtualenv
   pip install git+https://github.com/galaxyproject/planemo
   

8. Run the command to initialise a workflow test from the workflows/ subdirectory - if it doesn’t exist, you might need to create it first.

   planemo workflow_test_init --from_invocation <INVOCATION ID> --galaxy_url <GALAXY SERVER URL> --galaxy_user_key" <GALAXY API KEY>
   

   This will produce a folder of files, for example from a testing workflow:

   $ tree
   .
   ├── test-data
   │   ├── input dataset(s).shapefile.shp
   │   └── shapefile.shp
   ├── testing-openlayer.ga
   └── testing-openlayer-tests.yml
   

9. You will need to check the -tests.yml file, it has some automatically generated comparisons. Namely it tests that output data matches the test-data exactly, however, you might want to replace that with assertions that check for e.g. correct file size, or specific text content you expect to see.
10. Contribute all of those files to the GTN in a PR.

Still have questions?

Want to embed this snippet (FAQ) in your GTN Tutorial?

{% snippet  faqs/gtn/gtn_workflow_testing.md %}