Add BWA-MEM2 indexing tool

[mvdbeek]

Builds on #6558

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)

[bgruening]

Can we somehow reuse the data managers? It seems redundant to create a new index tool for all our reference consuming tools.

[mvdbeek]

I don't see how. You'd have to look at every data manager, exclude the parameters that are unsafe and then allowlist user execution. Picking up a directory from extra_files_path is way simpler.

[bgruening]

Somehow, I thought the plan was to enforce data-bundles for non-admin users and consume those data-bundles by tools. Did I mixed that up?

[mvdbeek]

That was the plan, but I don't think it's working out. It starts with data managers being pretty complicated to write, then you got a single extension .data_manager_json for all of the different table types, data managers can create more than one entry, the dbkey displayname etc values don't really make sense in the context of history items.

I think it would make more sense to go the other way around and have a data manager that knows how to consume datatypes like bwa_mem2_index and turns it into a loc file entry by adding the required metadata.