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List Experiment Files

encode_list_files
Read-onlyIdempotent

List and filter files from a specific ENCODE experiment by format, type, or category to identify relevant genomic data files.

Instructions

List all files for a specific ENCODE experiment, with optional filters.

Examples:

  • All BED files: experiment_accession="ENCSR133RZO", file_format="bed"

  • FASTQs only: experiment_accession="ENCSR133RZO", file_format="fastq"

  • Signal tracks: experiment_accession="ENCSR133RZO", output_category="signal"

  • Default/recommended files: preferred_default=True

  • Peaks from GRCh38: file_format="bed", output_type="IDR thresholded peaks", assembly="GRCh38"

Common file_format values: "fastq", "bam", "bed", "bigWig", "bigBed", "tsv", "hic"

Common output_type values: "reads", "alignments", "signal of unique reads", "signal of all reads", "fold change over control", "IDR thresholded peaks", "pseudoreplicated peaks", "replicated peaks", "gene quantifications", "transcript quantifications", "contact matrix"

WHEN TO USE: Use to browse files within a known experiment. Use encode_search_files instead to find files across experiments. RELATED TOOLS: encode_search_files, encode_get_file_info, encode_download_files

Args: experiment_accession: ENCODE experiment accession (e.g., "ENCSR133RZO") file_format: Filter by format ("fastq", "bam", "bed", "bigWig", "bigBed", etc.) file_type: Filter by specific type ("bed narrowPeak", "bed broadPeak", etc.) output_type: Filter by output type ("reads", "peaks", "signal", etc.) output_category: Filter by category ("raw data", "alignment", "signal", "annotation") assembly: Filter by genome assembly ("GRCh38", "hg19", "mm10") status: Filter by status ("released", "archived", "in progress") preferred_default: If True, return only default/recommended files limit: Max files to return (default 200)

Returns: JSON list of files with accession, format, size, download URL, and metadata.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
experiment_accessionYes
file_formatNo
file_typeNo
output_typeNo
output_categoryNo
assemblyNo
statusNo
preferred_defaultNo
limitNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

Annotations already provide readOnlyHint=true, destructiveHint=false, openWorldHint=true, and idempotentHint=true, indicating a safe, read-only, idempotent operation. The description adds context beyond this: it explains the default limit (200 files), provides examples of common parameter values, and describes the return format ('JSON list of files with accession, format, size, download URL, and metadata'), which is useful behavioral information not covered by 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 and front-loaded with the core purpose, followed by examples, common values, usage guidelines, related tools, and parameter explanations. Every section earns its place by providing actionable information 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 (9 parameters, 1 required) and the presence of annotations and an output schema, the description is complete. It covers purpose, usage, examples, parameter semantics, and return format, compensating for the 0% schema description coverage. The output schema handles return values, so the description doesn't need to explain them further.

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

Parameters4/5

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

Schema description coverage is 0%, so the description carries the full burden. It provides meaningful context for parameters: examples show how to use filters like file_format and output_type, lists common values for file_format and output_type, explains the purpose of preferred_default, and specifies the default for limit. This adds significant semantic value beyond the bare schema, though it doesn't cover all parameters in detail.

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: 'List all files for a specific ENCODE experiment, with optional filters.' It specifies the verb ('List'), resource ('files'), and scope ('for a specific ENCODE experiment'), and distinguishes it from sibling tools like encode_search_files, which searches across experiments.

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 includes an explicit 'WHEN TO USE' section: 'Use to browse files within a known experiment. Use encode_search_files instead to find files across experiments.' It names the alternative tool and clarifies the context, providing clear guidance on when to use this tool versus others.

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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