New Tool Coco2Labelme

[TuturBaba]

• 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 tool converts COCO annotation files (JSON) into LabelMe JSON files, one per image.

The SAM3 export creates results in COCO format. However, if you want to check or fix the annotations by hand using AnyLabeling, you cannot do this because AnyLabeling needs the LabelMe JSON format

Notes

• The code is based on cv_utils by WoodsGao (GPL-3.0). This tool is also released under GPL-3.0.
• The user can choose how the imagePath field is written in the output, to match different folder structures (simple, AnyLabeling default, or custom path).

[TuturBaba]

Hello @bgruening
I am having an issue with my GitHub tests:

mv: cannot stat 'tool_test_output.json': No such file or directory
mv: cannot stat 'tool_test_output.html': No such file or directory

A colleague is experiencing the same problem in the tools-iuc (galaxy.org) repository, but it doesn't happen every time.

[anuprulez]

Hello @bgruening I am having an issue with my GitHub tests:

mv: cannot stat 'tool_test_output.json': No such file or directory
mv: cannot stat 'tool_test_output.html': No such file or directory

A colleague is experiencing the same problem in the tools-iuc (galaxy.org) repository, but it doesn't happen every time.

I think I am also facing similar issues in my PR: #1817

Locally all tool tests and linting pass.

[SaimMomin12]

Hello @bgruening I am having an issue with my GitHub tests:

mv: cannot stat 'tool_test_output.json': No such file or directory
mv: cannot stat 'tool_test_output.html': No such file or directory

A colleague is experiencing the same problem in the tools-iuc (galaxy.org) repository, but it doesn't happen every time.

I think I am also facing similar issues in my PR: #1817

Locally all tool tests and linting pass.

We had some CI cache issues, let me try to re-trigger manually

[TuturBaba]

So normally, we can merge.
The lint error is due to the version:
ERROR (ShedVersion): yolo_predict: version 8.3.0+galaxy5 is less than or equal to the latest installable version 8.3.0+galaxy5.5

[bgruening]

The failing test looks relevant: https://github.com/bgruening/galaxytools/actions/runs/23297276348?pr=1816

[TuturBaba]

The failing test looks relevant: https://github.com/bgruening/galaxytools/actions/runs/23297276348?pr=1816

Oh yes I don't see sorry

[TuturBaba]

I changed compare = diff to contains so the test can pass. I’m not sure if this is a good idea. What do you think about it?
The error may be because GitHub adds a space. When I try to remove this space, I don’t see it in the file, but I see it in the HTML.

--- local_file
+++ history_data
@@ -3589,4 +3589,4 @@
   "imageHeight": 640,
   "imageWidth": 426,
   "text": ""
-} 
+}

Actually, I’m not sure if the problem is really a space. When I download the HTML, I see one, but maybe it is just because of the format.

[bgruening]

its probably not the space, but a line break.

You can generate this file with planemo test --biocontainers --update_test_data