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biocontext-ai

nucleotide_archive_mcp

get_download_urls

Obtain FTP download URLs for all sequencing data files in a study. Use after searching RNA studies to get direct links for file downloads.

Instructions

Get FTP download URLs for all sequencing data files in a study.

Usage Tips

Call after search_rna_studies() to get download URLs for selected studies. Returns FTP URLs that can be used with wget/curl or passed to generate_download_script().

Returns

dict Dictionary containing: - study_accession: Queried study - file_count: Total number of files - total_size_gb: Total download size in GB - runs: List of per-run file info, each with: - run_accession: Run identifier - file_count: Files in this run (2 for paired-end) - size_gb: Run size in GB - urls: List of FTP URLs (ftp://...) - md5_checksums: List of MD5 hashes (if include_md5=True) - message: Info message if no files found - error: Error message if any

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
study_accessionYesStudy accession from search results. Accepts SRP/ERP/DRP or PRJNA/PRJEB/PRJDB formats
file_formatNoFile format to download (fastq, submitted, or sra). FASTQ is most commonfastq
include_md5NoInclude MD5 checksums for file integrity verification

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries full burden. It details the return structure but does not explicitly state behavioral traits like safety (read-only), side effects, authentication needs, or rate limits. The return description hints at no destructive behavior, but this is not confirmed.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with sections (usage tips, returns). It is informative and avoids unnecessary fluff, though the returns section repeats information that may be in the output schema. Slightly more concise could be achieved.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given no annotations and the presence of output schema, the description covers inputs, usage, and outputs well. It mentions prerequisite (call after search) and provides detailed return structure. Lacks error handling details and authentication info, but is fairly complete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3. The description does not add new meaning to parameters beyond the schema, though the return section mentions include_md5 affecting checksums. Overall, it does not significantly enhance parameter understanding.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool gets FTP download URLs for sequencing data files in a study. It specifies the verb (get), resource (FTP download URLs), and scope (study). It implicitly distinguishes from siblings by mentioning usage after search_rna_studies and passing to generate_download_script.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly says 'Call after search_rna_studies()' and mentions alternatives: 'can be used with wget/curl or passed to generate_download_script()'. While it doesn't explicitly list when not to use it, the guidance is clear and contextual.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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