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Download ENCODE Files

encode_download_files
Idempotent

Download ENCODE files by accession to a local directory with MD5 verification, concurrent downloads, and flexible organization options.

Instructions

Download specific ENCODE files by accession to a local directory.

Downloads files from ENCODE to your local machine. Supports MD5 verification, concurrent downloads, and skip-if-already-downloaded.

WHEN TO USE: Use for downloading specific files by accession. For bulk downloads, prefer encode_batch_download. RELATED TOOLS: encode_batch_download, encode_search_files, encode_log_derived_file

Args: file_accessions: List of file accessions to download (e.g., ["ENCFF635JIA", "ENCFF388RZD"]) download_dir: Local directory path to save files (e.g., "/Users/you/data/encode") organize_by: How to organize downloaded files: - "flat": All files in download_dir (default) - "experiment": download_dir/ENCSR.../filename - "format": download_dir/bed/filename - "experiment_format": download_dir/ENCSR.../bed/filename verify_md5: Verify file integrity with MD5 checksum (default True)

Returns: JSON with download results for each file (path, size, success/error, MD5 status).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
file_accessionsYes
download_dirYes
organize_byNoflat
verify_md5No

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

The description adds valuable behavioral context beyond annotations: it mentions MD5 verification, concurrent downloads, skip-if-already-downloaded behavior, and organization options. Annotations provide hints (e.g., idempotentHint: true aligns with skip behavior), but the description elaborates on practical implementation details that enhance transparency.

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

Conciseness5/5

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

The description is well-structured and front-loaded: it starts with a clear purpose, followed by usage guidelines, related tools, and detailed parameter explanations. Every sentence adds value without redundancy, making it efficient and easy to parse.

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

Completeness5/5

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

Given the tool's complexity (4 parameters, 0% schema coverage, no output schema needed as returns are described), the description is complete. It covers purpose, usage, parameters, and return values, providing all necessary context for an AI agent to invoke the tool correctly.

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

Parameters5/5

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

With 0% schema description coverage, the description fully compensates by explaining all parameters in detail. It defines each parameter's purpose, provides examples (e.g., file accessions list, directory path), and explains enum values for 'organize_by' with clear descriptions of each option.

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's purpose with specific verbs ('download files') and resources ('ENCODE files by accession to a local directory'). It distinguishes from sibling tools by specifying it's for 'specific files by accession' versus 'bulk downloads' with encode_batch_download.

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

Usage Guidelines5/5

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

The description explicitly provides usage guidance with a 'WHEN TO USE' section that states 'Use for downloading specific files by accession. For bulk downloads, prefer encode_batch_download.' It also lists related tools, offering clear alternatives and context.

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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