Suggestion for an order of IDs/links annotations

[matuskalas]

... and added the missing xrefs.

This is based on a chat with @bgruening in winter 2020, and is also what I've been following when annotating example IUC tools. The idea was to have all the IDs a.k.a. external links a.k.a. upstream annotation next to each other: xrefs, edam_topics, edam_operations, citations.

If the order should be changed as suggested, it might be good to also change it in: (I volunteer if green light)

• https://docs.galaxyproject.org/en/latest/dev/schema.html (Is that just https://github.com/galaxyproject/galaxy/blob/dev/doc/schema_template.md?)
• https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/xsd/galaxy.xsd (Note: the XML schema itself is order-agnostic)
• Anywhere else?

[bgruening]

Thanks @matuskalas for bringing this up. This here needs also to be changed: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/linters/xml_order.py

[wm75]

:+1: for grouping these elements +0.5 for moving the group to the end of the tool definition because that would allow the citations element to stay in its familiar place

Within the group, I'd have a slight preference for moving xrefs below the edam elements and have it just above the citations. I think that may be more intuitive since the citations are typically for the command line tool pointed to by xrefs. It's also the order currently described in the tool xml syntax.

[Slugger70]

A good idea to put them all together. I agree with Wolfgang's order of placement.

[matuskalas]

Excellent, thanks for the replies!

As I understood, the currently winning order would be edam_topics, edam_operations, xrefs, citations, all of it towards the end after help. Right?

(Another consideration would be having it all up between description (which they are kind-of extension of) and macros, but that would mean moving citations to the other end.)

I can fix it all over & PR, probably tonight...

[wm75]

As I understood, the currently winning order would be edam_topics, edam_operations, xrefs, citations, all of it towards the end after help. Right?

Yes, this is what I have in mind.

[annefou]

@matuskalas As suggested by @bgruening I can add in the documentation some information about EDAM popovers. Does it make sense? If yes, what would be best: make a PR to matuskalas:patch-1 to get it in this PR or to make a separate PR.

[matuskalas]

Whichever you prefer @annefou :-)