object output from PAGA plotting

[pinin4fjords]

Description

This is the Galaxy component of ebi-gene-expression-group/scanpy-scripts#95. Essentially configuring the PAGA plotting to output an object alongside the plotfile, which can then be used for initialising FDG.

Fixes # (issue)

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Checklist

• I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
• If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
• If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1)

[pcm32]

Could we smuggle here the change of the last citation to our nature methods?

<citation type="doi">10.1101/2020.04.08.032698</citation>

I tried committing it myself, but for some reason it doesn't allow me to write to it ¿?.

[pinin4fjords]

We appear to be suffering from issues like those reported in galaxyproject/planemo#1078. Trying to think of a way of working around them here.

[pinin4fjords]

I think the MNN issues preventing the CI passing are down to a numpy problem- I've tried to apply a fix in a new build of scanpy scripts bioconda/bioconda-recipes#27908

[pinin4fjords]

Okay, we can't actually skip single tools yet (see galaxyproject/planemo-ci-action#13).

@pcm32 the test for MNN passes locally, and the trajectory plotting passes here (which is what this PR should be about). Can we override the CI and merge this for now, in the interests of getting this functionality out there? I don't have more time to spend on the MNN instruction error thing.

[pcm32]

LGTM, please bump the version to reflect the scanpy version as suggested.

[pcm32]

Just to make a note that the copy from FTP code is here.

[pinin4fjords]

Okay, looking good now I think. I'll keep an eye and see if the deploy works, of if I'll have to update as I've done in pr.yaml.