I’m currently wrapping a tool and running into an issue with the output files during testing. When I run planemo test with the --no_cleanup flag, I can see that the output files are correctly generated inside the temporary working directory. However, these files don’t appear in my test-data directory, and as a result, the tests always fail.
When I use the --update_test_data flag, the expected output files are created in test-data, but they are unfortunately empty.
You can find more complex examples in the ToolShed as well. Try finding a tool that is similar to yours then navigate from the tool form Options menu. You can explain what your tool does and we can try to help to find an example that matches, too.
My first guess is that since the test-data outputs are getting a label (an output file name that you are creating) but not any content, yet you are seeing the output in other ways, maybe that data content and the “output file name” are not getting a connection for some reason. Sometimes this is a simple mapping and sometimes the expressions are more complex but there could also be a small typo. I’m not sure if a mismatched datatype would result in the content not moving over at all but that seems possible depending on the file compression involved and what exactly is being done, if anything, as a post processing step before populating the result back.
Please give that a try if you haven’t yet. If you want to share back that section of your script along with the full file name in the output directory, we might be able to help more. You can format quoted text here or share a link to Github or a Gist.
