Galaxy: Replace tool panel sections with EDAM

[hexylena]

Since I proposed this in the round table, figured I'd document my vision here a bit.

Background

We need a solution for the tool panel sections. They're non-uniform, they're hard to categorise properly, everyone does their own thing, it's a mess. Every admin needs to decide for themselves where the tool should go and they aren't always the best people to make that decision (speaking for myself here, I know nothing about where some rna tools go.)

Solution

Burn the tool_conf, shed_tool_conf, and integrated tool panel to the ground. Instead, we rely primarily on the EDAM terms sourced from the tools. For every EDAM term, users will see a "section" in Galaxy. We can natively nest these based on the EDAM hierarchy.

Now, we just have: the list of tools installed (shed database, maybe a list of tools in a tooL_conf like file.) And we have the EDAM terms.

Possible Issues

1. Tools aren't annotated with EDAM. Great, we should fix this. Throwing anything without tags in an "UNCATEGORISED" section at the end will be good motivation.
2. Old tools aren't annotated. Let's update them. Tools generally won't change EDAM types over time, so if any of the versions in the lineage are annotated with some tags, then we can take those.
3. Admins want their own sections? @jmchilton proposed that we permit additional ontologies that can be used, and admins can tag these tools (either in the tool, or outside in the database?)

Benefits

• No more shed_tool_conf or ITP. @natefoo, @Slugger70 and other admins everywhere rejoice :tada:
• Better EDAM annotation of existing tools
• Hierarchical tool panel
• Users can find tools by well annotated "thing I want to do", and can find them across every applicable section.

[hexylena]

Starting places for work:

Review these!

• [ ] galaxyproject/tools-iuc#1905
• [ ] galaxyproject/tools-iuc#1897

Implement this:

• [ ] expose edam in toolbox
• [ ] new toolbox based around edam.

[bgruening]

ping @hmenager @matuskalas

[hexylena]

ping @inkuzmin

[innovate-invent]

I would caution against having tools listed within the edam tree. It could get annoying to find deeply nested tools.
Having a edam tree view adjacent to a flat tool list, which is then filtered by the selection in the tree would be better.
This allows tools that are annotated by a sub type to be listed when a parent type is selected.
It also provides the opportunity to collapse the tree view and have a simple search box at the top of the tool list.

[hexylena]

A flat list would definitely be my desired entrypoint! a tree only as a second view if development time would not be excessive.

[hmenager]

I completely agree with warnings related to any overly complex UI. The UI should:

• still be "simple", e.g. as flat as possible
• be customisable, but not ask users anything complex like providing an ontology to get it.

So:

• step #1 annotate properly a significant set of IUC tools
• step #2 prototype a bit to see how the resulting tool panel could look like
  and then, start implementation.

I'll be happy to help in any way.

[hexylena]

I think I might have motivation to work on the galaxy portion of this a bit? If there's no PR in the next two weeks, anyone else should feel free to take over :)