docs: give the WDL quickstart example a version and test it

[vshulcz]

Changelog Entry

To be copied to the draft changelog by merger:

• The WDL quickstart example now specifies a WDL version and is covered by a test.

Description

Fixes #5534.

The WDL in the quickstart has no version, so it is parsed as draft-2 and toil-wdl-runner fails on it:

(Ln 1, Col 1) MissingVersion, document should declare WDL version; draft-2 assumed
WDL.Error.EvalError: Cannot evaluate no expression for message

The inputs JSON also addresses the task input directly (write_simple_file.write_file.message), which does not bind.

This ports the example to WDL 1.0 (input sections, ~{} placeholder, the call passing message through), so the inputs file uses write_simple_file.message.

To keep the docs and a tested file from drifting apart, the example now lives in src/toil/test/docs/scripts/ next to the other documentation examples and is pulled into quickStart.rst with literalinclude. MANIFEST.in already ships that directory. test_documentation_quickstart in wdltoil_test.py runs it the same way test_MD5sum runs its workflow.

Verified locally on an Apple Silicon macOS host with Docker:

$ toil-wdl-runner wdl-helloworld.wdl wdl-helloworld.json -o out --logDebug --retryCount=0
Workflow stopped. Success: True
{"write_simple_file.write_file.test": ".../out/write_simple_file.write_file/wdl-helloworld-output.txt"}
$ cat out/write_simple_file.write_file/wdl-helloworld-output.txt
Hello world!

$ pytest src/toil/test/wdl/wdltoil_test.py -k test_documentation_quickstart -x -q
1 passed, 35 deselected

I left make format alone: black --check already reports wdltoil_test.py as unformatted on unmodified master here, so running it would bury this change in unrelated reformatting.

[adamnovak]

This looks OK to me.