hopefully fixes lastz PAF output

[scottcain]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[bernt-matthias]

Please add a test case.

[scottcain]

@bernt-matthias while I agree with the sentiment of adding a test case, I feel trapped in a bit of a catch 22: I don't have a way to run lastz and have it produce PAF output to put in a test to compare to, which feels required for writing a real test.

A minor additional issue is that I have no idea how to write tests in this framework, but that is at least surmountable.

Do you have any suggestions?

[scottcain]

/me thinks to himself "there's probably a container somewhere that I could run interactively to make it do this" (but I don't know anything about that either, so I need guidance to get that far too)

[bernt-matthias]

I see :) It's quite easy if you can run planemo.

Add a test case (e.g. by copy pasting one of the existing) that sets the output_format parameter (crazy that there is none so far) change the filename of the output in the test and run

planemo test --biocontainers tools/lastz/lastz.xml --update_test_data

Let us know if you need help or just don't have the time.