EDAM annotation in XML tool definition vs bio.tools

I had a discussion with Bérénice yesterday and it was suggested that I create an issue here to further discuss things.

AFAIK the Codex uses the EDAM annotations from bio.tools and ignores those in the XML tool definitions. However, there are numerous Galaxy tools in our community which wrap around a single tool in terms of bio.tools, e.g., [scikit-image](https://bio.tools/scikit-image), which is a very generic library for image processing, image analysis, and visualization.

For those Galaxy tools, there are, for example, [Filter 2-D image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_simple_filter%2Fip_filter_standard) and [Compute Voronoi tessellation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fvoronoi_tesselation%2Fvoronoi_tessellation). Both wrap around scikit-image, both inherit the EDAM annotations from scikit-image, right? However, [Filter 2-D image](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2F2d_simple_filter%2Fip_filter_standard) is a tool for image processing and certainly not analysis, while [Compute Voronoi tessellation](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fvoronoi_tesselation%2Fvoronoi_tessellation) is rather associated with image analysis than processing.

The question now is, how can we establish a finer level of granularity for Galaxy tools? One the one hand, it seems natural to not ignore the EDAM annotations in the Galaxy tool wrappers, but to give them precedence. On the other hand, this might be dangerous because the EDAM annotations in bio.tools are usually more reliable. Maybe, the middle ground here is to give precedence to the EDAM annotations in the Galaxy tool wrappers only for specific tools (those which are too generic).

xref https://github.com/beatrizserrano/BH2024-project17/issues/1

Start by tracing how the Codex currently reads EDAM annotations from bio.tools and compare that behavior with the XML tool definitions and linked examples. Resolve the precedence and granularity policy, then verify that the chosen approach distinguishes the Filter 2-D image and Compute Voronoi tessellation cases.

Written by the indexing model from the issue text.