galaxyproject / galaxyproject/galaxy_codex
Tool ID column in curated tools doesn't expand macros in tool_id
- Dominant language
- HTML
- Stars
- 28
- Forks
- 36
- Avg merge
- 19h 29m
- Merged PRs (30d)
- 1
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
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