Add bioproject2srr and srr2sam Galaxy tools for NCBI metadata retrieval#1
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Add bioproject2srr and srr2sam Galaxy tools for NCBI metadata retrieval#1crashfrog wants to merge 2 commits into
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…Projects Retrieves SRR accessions and biosample metadata from NCBI BioProjects using Entrez E-utilities API. Recursively follows links to subprojects and biosamples. Outputs: - accessions.txt: deduplicated list of SRR accessions - metadata.tsv: full metadata table joining biosample attributes with SRA runs Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Adds complementary tool that retrieves BioSample metadata from a list of SRR accessions. Performs reverse operation of bio2srr by traversing NCBI Entrez from SRA to BioSample. Output: tabular file with SRR accession as first column followed by all BioSample metadata fields. Also adds CLAUDE.md documentation covering both tools' architecture, testing, and constraints. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Summary
bioproject2srr
Recursively follows links from BioProject → subprojects → BioSamples → SRA runs.
Outputs:
accessions.txt: deduplicated list of SRR accessionsmetadata.tsv: full metadata table with biosample attributes joined to SRA run informationsrr2sam
Traverses from SRR → SRA → BioSample to retrieve metadata.
Output:
output.tsv: tabular file with SRR accession as first column, followed by all BioSample metadata fieldsTesting
Documentation
Includes CLAUDE.md with architecture details, testing commands, and API usage patterns.
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