Add collapse_collection tool with polished UI and help#7810
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nekrut wants to merge 7 commits intogalaxyproject:mainfrom
Open
Add collapse_collection tool with polished UI and help#7810nekrut wants to merge 7 commits intogalaxyproject:mainfrom
nekrut wants to merge 7 commits intogalaxyproject:mainfrom
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Imported from phac-nml/galaxy_tools, renamed merge.xml to collapse_collection.xml. Rewrote help with structured Synopsis/Description/Examples format. Added inline SVG diagram via macros.xml. Improved input labels and help attributes. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
bgruening
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Mar 22, 2026
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Replace raw HTML SVG with PNG via $PATH_TO_IMAGES - Ship SVG source in static/images/ - Remove display="checkboxes" from one_header - Clean up output tag (self-closing) - Add citation for phac-nml/galaxy_tools - .shed.yml: add long_description, remote_repository_url, homepage_url Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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bernt-matthias
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bernt-matthias
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Isn't this the same as https://toolshed.g2.bx.psu.edu/repositories/12213e550a6c4a72
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
| preserving collection order. Supports header deduplication and dataset name | ||
| prepending in several placement modes. | ||
| name: collapse_collections | ||
| owner: iuc |
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Mu suggestion would be
Suggested change
| owner: iuc | |
| owner: nml |
otherwise there will be two collapse_collections tools in the future. But this will only work if nml grants write access to the toolshed repo.
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@nekrut we need to solve this. We should not break the tool lineage.
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This is one of the foundational collection tools. It lived in https://github.com/Takadonet but should be brought into iuc. This PR does that and makes UI much less confusing.
Summary
collapse_collectiontool from phac-nml/galaxy_toolsmerge.xmltocollapse_collection.xmlfor consistency with tool idmacros.xmltoken) illustrating header merging with dataset name prependingTest plan
planemo l— lint passes (remaining warnings are pre-existing: boolean conditional, no citations)planemo t— all 3 tests pass🤖 Generated with Claude Code