Galaxy Tools

Galaxy wrappers and wrapper prototypes for biomedical data analysis.

This repository is intended to live under goeckslab and follow the broad pattern used by community Galaxy wrapper repositories: one tool directory per wrapper, Tool Shed metadata in each directory, Planemo lint/test support, and small committed test data where possible.

Tool Index

Tool	Purpose	Dependency strategy
featurewise_correlation	Compute one Spearman or Pearson correlation test per matched feature across two matrices, with multiple-testing correction.	gseapy=1.2.1 package requirement for a BioContainer-backed SciPy runtime.
gseapy_enrichr	Run GSEApy Enrichr-style over-representation analysis from a Galaxy gene list, named Enrichr libraries, or uploaded GMT files.	gseapy=1.2.1 package requirement.
kegg_ora	Run KEGG-style pathway over-representation analysis from foreground/background gene lists and a gene-to-pathway mapping.	python=3.11 package requirement, resolving to the Python BioContainer.
nonparametric_rank_tests	Run independent Mann-Whitney U tests and paired Wilcoxon signed-rank tests on tabular data.	gseapy=1.2.1 package requirement for a BioContainer-backed SciPy runtime.
phykit_metrics	Expose selected PhyKIT tree and alignment metrics for single files, collections, grouped collections, ZIP archives, or grouped ZIP archives.	phykit=2.1.93 package requirement.
rds_to_tabular	Convert RDS/RData objects containing rectangular R data into Galaxy tabular datasets.	bioconductor-deseq2=1.42.0 package requirement for a BioContainer-backed R environment.

Development

Use the project virtual environment from the repository root:

.venv/bin/planemo --version

Run Planemo lint for every wrapper:

for tool in tools/*/*.xml; do
    .venv/bin/planemo lint "$tool"
done

Run Tool Shed lint for every tool directory:

for repo in tools/*; do
    .venv/bin/planemo shed_lint "$repo"
done

Run a focused wrapper test:

.venv/bin/planemo test --conda_auto_install tools/kegg_ora/kegg_ora.xml

For usegalaxy.org-oriented checks, prefer testing the same container resolution path Galaxy will use. For example, kegg_ora should resolve python=3.11 to quay.io/biocontainers/python:3.11:

TMPDIR="$HOME/.tmp/planemo-galaxy-tools" \
    .venv/bin/planemo test --docker tools/kegg_ora/kegg_ora.xml

Current Status

• featurewise_correlation: Planemo lint and fixture tests pass locally; the wrapper declares GSEApy as a package requirement to resolve a BioContainer that includes SciPy, instead of forcing an explicit container.
• gseapy_enrichr: Planemo lint, Tool Shed lint, and the committed GMT fixture test pass locally; dependency resolution can use the existing GSEApy BioContainer.
• kegg_ora: Planemo lint, Tool Shed lint, direct fixture checks, and Docker Planemo tests pass locally; malformed non-empty gene-list rows fail clearly.
• nonparametric_rank_tests: Planemo lint, Tool Shed lint, and fixture tests pass locally; grouped-table Wilcoxon input is rejected because it has no pair identifier, and the wrapper declares GSEApy as a package requirement to resolve a BioContainer that includes SciPy, instead of forcing an explicit container.
• phykit_metrics: Planemo lint, Tool Shed lint, and fixture tests pass locally with Galaxy-managed dependencies, including collection and grouped-collection batch modes. ZIP and grouped-ZIP convenience modes are also covered by fixture tests.
• rds_to_tabular: Planemo lint, Tool Shed lint, and fixture tests pass locally; list extraction and RData object-name handling have targeted regression coverage.