Genomics MCP

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fetch_file

Download a genomic file and its index into your local work directory as a bounded transfer job; specify budget_bytes for files above the default limit.

Instructions

Start a bounded download of a file (and index) to the local work dir. Returns a transfer job; files above the default limit need budget_bytes. Available for: default.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`file`	Yes
`prepare`	No
`budget_bytes`	No
`include_index`	No
`verify_checksum`	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 / prepare

Added value: +{
+  "default": false,
+  "title": "Prepare",
+  "type": "boolean"
+}

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

A3.6/5.0

Behavior4/5

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

Annotations cover the safety profile (readOnlyHint=false, destructiveHint=false, openWorldHint=true), and the description adds genuinely new behavioral context: the download is bounded, it also grabs the index, it is asynchronous (returns a transfer job), and the size limit requires budget_bytes. It omits failure/retry semantics and whether re-issuing is idempotent, so not a 5.

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?

Two efficient, front-loaded sentences with no filler; the core action and return type come first. The trailing 'Available for: default' is cryptic and slightly dilutes the otherwise tight structure.

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-value detail is appropriately omitted and 'Returns a transfer job' suffices. However, for a 5-parameter mutation/transfer tool with 0% schema description coverage, the description should at least clarify prepare and verify_checksum, which it does not.

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?

Top-level schema description coverage is 0%, so the description must compensate. It adds meaning for budget_bytes (the size-limit override) and include_index (the '(and index)' clause), but leaves prepare and verify_checksum entirely unexplained in both schema and description.

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+resource ('Start a bounded download of a file (and index) to the local work dir') and the return shape ('Returns a transfer job'). It is distinguishable from siblings like get_transfer_status and cancel_transfer, though it never names them or any 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?

Implies usage (download a file locally, e.g. before read-level tools that require local data) but never states when to use this vs. the sibling access tools. The only concrete guidance is the conditional 'files above the default limit need budget_bytes', and 'Available for: default' is opaque.

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