tools: add 3dtrees metadata wrapper - #2
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Updated the annotation_path parameter to include 'tgz' format.
Updated version suffix and modified interpolation parameter settings.
* Update 3dtrees_raycloudtools to version 1.2.0 * Update test data
* Update RAG embedding model filter tag from 'embedding' to 'vector-rag' * Update huggingface.loc.sample: use 'vector-rag' free_tag for RAG embedding models
…ools/ribotaper Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1
Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
The XML declares format="markdown" but valid_file_types checked for "md", causing "Unsupported file type: markdown" when selecting markdown datasets. Align the Python check with the Galaxy format name. Bump galaxy version suffix 0 → 1.
…ad_embeddings.py (bgruening#1858) SentenceTransformer.save() rewrites modules.json with deep class paths (e.g. sentence_transformers.base.modules.transformer.Transformer) that don't exist in older ST versions. The Galaxy container has ST 5.3.0 which cannot import sentence_transformers.base, causing ModuleNotFoundError. snapshot_download preserves the HF Hub files byte-for-byte, keeping the stable sentence_transformers.models.* paths that work across all ST 5.x. Also adds PEP 723 inline script metadata so uv run resolves deps without --with flags, shrinking the dependency from sentence-transformers (50+ packages including torch) to just huggingface_hub.
…ning#1857) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
* Fix Tiara wrapper when outputs are missing * Address the comments * edited the framework and test * tiara wrapper fixes
Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
* Update mafft.xml * Update VERSION_SUFFIX token to 3 --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Fix `no_interp` parameter in Cellpose-SAM wrapper
* updated opsin and added shed.yml file * fixed url * Update chemicaltoolbox/opsin/opsin.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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Summary
Adds a new
3dtrees_metadataGalaxy wrapper for the 3Dtrees metadata extraction tool.The wrapper reads a
collection_summary.json, computes the centroid ofcollection.multipolygon_wkt, and extracts selected metadata layers intoadditional_metadata.json.Included Metadata Layers
Both layers are exposed as a required multi-select in Galaxy, with both selected by default. The reference datasets are optional inputs and are only passed to the tool when their corresponding layer is selected.
Tool Repository
The tool implementation is released at:
https://github.com/3dTrees-earth/3dtrees_metadata/releases/tag/v1.0.0
Validation
tools/3dtrees_metadata/3dtrees_metadata.xmlmake tool-test-3dtrees_metadata PLANEMO_GALAXY_ROOT=/tmp/planemo-3dtrees-metadata-galaxy-5Planemo result:
3dtrees_metadataboth layers: passed3dtrees_metadataGADM-only: passed3dtrees_metadataecoregion-only: passed