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Download ENCODE Files

encode_download_files
Idempotent

Download specific ENCODE files by their accession numbers to a local directory, with MD5 verification and optional organization by experiment or format.

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., "./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
Behavior5/5

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

The description discloses MD5 verification, concurrent downloads, and skip-if-already-downloaded behavior. Annotations indicate readOnlyHint false, destructiveHint false, idempotentHint true, openWorldHint true, with no contradictions. The description adds valuable context beyond annotations.

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 with a brief summary, detailed features, usage guidance, and a parameter list. It is concise, with no extraneous information, and each sentence adds value.

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 4 parameters, 0% schema coverage, output schema presence, and annotations, the description provides complete guidance: parameter details, return format, and behavioral traits. Nothing essential is missing.

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?

Despite 0% schema description coverage, the description includes a detailed 'Args' section explaining each parameter with examples, defaults, and enum options for 'organize_by'. This fully compensates for the missing schema descriptions.

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 name and title clearly indicate downloading ENCODE files. The description specifies 'Download specific ENCODE files by accession to a local directory,' using a specific verb and resource, and distinguishes from sibling tools like 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 states 'WHEN TO USE: Use for downloading specific files by accession. For bulk downloads, prefer encode_batch_download.' It also lists related tools, providing clear guidance on when to use this tool versus alternatives.

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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