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list_files

Read-only

List files in a study or dataset with format, size, checksums, index, and readiness across EGA, ENA, ENCODE, GEO, local, NCBI Datasets, or S3 sources.

Instructions

List files of a study/dataset with format, size, checksums, index and readiness. Available for: ega, ena, encode, geo, local, ncbi_datasets, s3.

Input Schema

TableJSON Schema

Name	Required	Description
`cursor`	No
`source`	Yes
`formats`	No
`accession`	Yes
`max_records`	No	Lower the record limit.
`storage_profile`	No

Output Schema

TableJSON Schema

Name	Required	Description	Default
`data`	No
`error`	No	Set when status is error.
`errors`	No	Per-source failures in partial results.
`limits`	No
`status`	Yes
`warnings`	No
`operation`	Yes
`provenance`	No
`truncation`	No
`source_status`	No
`schema_version`	No		1
`metadata_omitted`	No	Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedv0.1.1Sep 28, 2026

addedInput schema / properties / storage_profile

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Storage Profile"
+}

addedOutput schema / properties / metadata_omitted

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": {
+        "type": "integer"
+      },
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Entries dropped from provenance/source_status/errors/warnings (or text shortened) to fit max_response_bytes. Absent when metadata is complete.",
+  "title": "Metadata Omitted"
+}

First observedv0.1.0Sep 24, 2026

TDQS

A3.5/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered. The description adds the returned-field inventory (checksums, index, readiness) and the supported-source constraint, but says nothing about pagination via cursor, authentication per source, or rate limits.

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?

Two short sentences with the core purpose front-loaded and the source constraint immediately after. No filler, no restatement of the tool name.

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

Completeness3/5

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

An output schema exists, so return values need not be described, and the source enumeration is useful. Still, for a 6-parameter tool with 17% schema coverage, the pagination cursor and storage_profile parameters are left entirely undocumented.

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 only 17%, so the description must carry more, and it partially does: it enumerates valid source values that the schema leaves as a bare string. But accession, cursor, storage_profile, formats filtering, and max_records semantics remain unexplained in both places.

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

Purpose4/5

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

States a specific verb (list) and resource (files of a study/dataset) plus the fields returned (format, size, checksums, index, readiness). It is clearly distinct from siblings like list_samples, list_sources, and describe_dataset, though it never names an alternative explicitly.

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

Usage Guidelines3/5

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

The 'Available for: ega, ena, encode, geo, local, ncbi_datasets, s3' line gives real context about when this tool applies, which is more than nothing. However, there is no when-not guidance, no mention of how this differs from describe_dataset, and no routing advice for choosing among sources.

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