Update anndata - galaxy version 1

[nilchia]

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)

This PR updates anndata with:

1. when renaming the categories, user can specify if they want to create a new key or just update the previous key
2. User can use different keys in adata.var to flag genes (to flag not only based on var names)
3. inspect anndata order is changed so it is less likely for the user to select "the full data matrix"

Thanks @nomadscientist for these nice suggestions ❤️

[nilchia]

@nomadscientist also suggests putting the anndata filter in the scanpy filter section.
I don't know if we should do it because they are from different tool suits, however, this filter option is not a method (API) from anndata but our own script. So maybe we can put it in scanpy tool suit?
What do you say @bgruening @pavanvidem?

[nomadscientist]

Oh this is super exciting!!!! Well done! Amazing!
And great catch on finding out that the filter function there is a Galaxy thing, rather than a Scanpy thing. I think that makes it much more reasonable to include, and then from a user perspective, all the FILTER functions are in the same tool (the Filter tool), then that makes a lot more sense for users.

[pavanvidem]

Sure, I will move the filter to scanpy filter tool and add a few more metadata copying functions

[pavanvidem]

Filter functions moved: #6648

[pavanvidem]

Hopefully, this PR covers most of the functions needed to update the tutorials. Tests need to be added.

[nilchia]

I don't know why cheetah complains on test 19.

[nilchia]

@pavanvidem should I add more tests?

[pavanvidem]

The tests seem to cover all the new features. Ready from my side. Thanks!

[bgruening]

Can you please check for spelling one last time. Otherwise, ready to go.

[nilchia]

I think we're good now.

[mvdbeek]

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/12727276627