New tool: Edit Coco Annotation

[TuturBaba]

Features

• Filters and renames tracks in a COCO JSON annotation file produced by SAM3 or any COCO-format
  • Mode Keep: only the listed track IDs are kept; all others are removed (+ optional: rename | frame_min | frame_max)
  • Mode Remove: only the listed track IDs are deleted; everything else is kept (+ optional: frame_min | frame_max)
  • Mode Rename: all tracks are kept, but listed IDs receive a new category name

Tests

Test 1: keep mode — keep track IDs 2, 4–6 and track ID 1 renamed to "Algae"
Test 2: remove mode — remove track ID 1 from frame 130 onwards
Test 3: rename mode — rename track ID 1 to "Algae" and track IDs 2–6 to "Crangon crangon"

[TuturBaba]

Hi if you can add skip-version-check pls

[SaimMomin12]

@TuturBaba

+Linting tool /home/runner/work/galaxytools/galaxytools/tools/image_processing/yolo/edit_coco_annotation.xml
Failed linting
.. CHECK (TestsNoValid): 3 test(s) found.
.. INFO (OutputsNumber): 1 outputs found.
.. INFO (InputsNum): Found 11 input parameters.
.. CHECK (HelpPresent): Tool contains help section.
.. CHECK (HelpValidRST): Help contains valid reStructuredText.
.. CHECK (ToolIDValid): Tool defines an id [edit_coco_annotation].
.. CHECK (ToolNameValid): Tool defines a name [Edit COCO Annotation].
.. CHECK (ToolProfileValid): Tool specifies profile version [25.1].
.. CHECK (ToolVersionValid): Tool defines a version [1.0.0].
.. INFO (CommandInfo): Tool contains a command.
.. WARNING (CitationsMissing): No citations found, consider adding citations to your tool.

[TuturBaba]

For me It's fine

[SaimMomin12]

Suggested change

	<tool id="edit_coco_annotation" name="Edit COCO Annotation" version="1.0.0" profile="25.1">
	<tool id="edit_coco_annotation" name="Edit COCO Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

Please use the above tokens

[TuturBaba]

Ok, but why?
If I use this method, I need to add the following block ?

<macros>
    <token name="@TOOL_VERSION@">1.0.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">25.1</token>
</macros>

Doesn't that come down to the same thing in the end?

[TuturBaba]

Hi @SaimMomin12,
Should I also apply these changes to my new tool that was merged yesterday (so not yet available on Galaxy)?
#1892

[bgruening]

@TuturBaba maybe we did a mistake here. Are those coco tool in anyway related to YOLO?

We group Galaxy tools together into so called tool-suites. Those tools share functionality/parameters/requirements and are located in one folder.

That is why we usually have the same version number, same profile etc.