galaxyproject / galaxyproject/galaxy_codex

Tool ID column in curated tools doesn't expand macros in tool_id

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Description

Some tools (see https://github.com/galaxyproject/tools-iuc/blob/main/tools/dimet/dimet_abundance_plot.xml) use macros in the tool id, which are not expanded when creating the curated tools table (see https://github.com/hechth/galaxy_codex/blob/ef45ad8d7cf1555dfa50f923679a024b9b9f3b72/communities/workflow4metabolomics/resources/curated_tools.tsv?plain=1#L9).

Ideally the macros should be expanded before the tool xml file is read to extract the tool id - or are they obtained from the toolshed somehow?

Contributor guide

Open the contributing guide

Research direction

Compare the macro-based tool ID in tools/dimet/dimet_abundance_plot.xml with the incorrect entry in communities/workflow4metabolomics/resources/curated_tools.tsv. First trace how the curated tools table reads tool XML and obtains IDs; determine whether macro definitions are available locally or through the Tool Shed. Done means the table records the expanded tool ID for macro-based tools without breaking existing entries.

Written by the indexing model from the issue text.

Assessment

Tech stack
xml
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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