Enhancement: Clarify mutually exclusive pipeline options on the SPADes tool form + fix non-submission bug

[jennaj]

Usage issue: some options on the form require the specification of other options and some are incompatible. Some of those incompatible options will not even produce an output dataset (see screenshots below, the whole submission is just aborted).

Suggestion: clarify this in the help text for the options, and possibly don't allow the job to submit at all (with a warning highlighting the issue) if incompatible options are selected or if required co-options are not specified. This should take into account any default options applied.

And, some incompatible combinations of options will submit but not actually produce outputs! No messages to the user about what might be going on, instead it looks like something is wrong with Galaxy itself.

Reported at https://help.galaxyproject.org/t/error-in-running-spades-assembly/14660/

Testing histories:

• https://usegalaxy.org/u/jen-galaxyproject/h/test-spades-options
• https://usegalaxy.eu/u/jenj/h/imported-from-archive-test-spades-options

SPADes guide: https://ablab.github.io/spades/running.html

Examples:

• Default works fine, and assembly+correction + careful works fine

• Then assembly+correction + careful + isolate will fail. This one does have a clear error message but the user only finds out after the job submitted. Could this be clarified better on the form, and prevent the job from submitting at all?

• And there is at least one combination that will not work but still sort of partially submits the job: only-error-correction + careful. It would be better if the invalid parameter combination fails on the form with a warning about what is going on instead, yes?

Screenshot of what that partially submitted job looks like at ORG

Screenshot of what that partially submitted job looks like at EU

• Finally, we had a report of a problem including careful that failed for the user with a slightly different message about the "mode" not being specified, which means the defaults were used, but they didn't get anything actionable. Maybe they will share the exact parameter combination so we can address that as well.