Add coordinate scaling tool to Galaxy mti-utils - Githubissues

goeckslab / tools-mti

MIT License

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Add coordinate scaling tool to Galaxy mti-utils #82

Closed CameronFRWatson closed 3 months ago

CameronFRWatson commented 3 months ago

Adds a tool for scaling the X,Y coordinates in single-cell data extracted from multiplex tissue imaging assays, in Anndata h5ad format. This allows for downstream spatial analysis that uses physical distances (i.e microns) rather than pixels which differs between imaging modalities. This PR also updates the mti-utils Docker image, and applies a few small changes to existing utils tools to accommodate the dependency updates.

This PR is related to

[x] Adding a new tool
[x] Updating an existing tool to a newer version
[ ] Fixing a bug or updating just the Galaxy wrapper of an existing tool
[ ] Making a change to the tools-mti repo, CI, or other misc. change

If updating an existing tool to a newer major version

[x] I have updated the TOOL_VERSION token in the tool's macros file
[x] I have reset the VERSION_SUFFIX to 0 in the tool's macros file

Provide details here

Requirements update details:
- New base image (Python 3.11)
- Added Anndata
- Pinned newer versions for all other existing dependencies

CameronFRWatson commented 3 months ago

I added a fix to issue https://github.com/goeckslab/tools-mti/issues/61 to this PR out of convenience. More minor changes to existing mti-utils