amr-mcp

run_amrfinder

Read-only

Screens local nucleotide or protein FASTA files for antimicrobial resistance genes and point mutations using a local AMRFinderPlus installation.

Instructions

Screen a local genome or proteome for AMR genes with AMRFinderPlus (must be installed locally).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "fasta_path": "<fasta_path>"
    },
    "name": "run_amrfinder"
  }
}

Input Schema

Name	Required	Description	Default
`organism`	No	Enables point-mutation screening, e.g. 'Escherichia', 'Klebsiella_pneumoniae'
`fasta_path`	Yes	Absolute path to a local FASTA file
`sequence_type`	No		nucleotide

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.3Nov 5, 2026

TDQS

A3.6/5.0

Behavior3/5

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

The annotations already establish readOnlyHint=true and openWorldHint=false, so the safety posture is covered. The description adds the meaningful prerequisite that AMRFinderPlus must be installed locally, but it does not disclose runtime behavior, failure modes, or computational cost beyond that.

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 a single front-loaded sentence with no filler. Every phrase contributes to purpose, input scope, or the local-install constraint.

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

Completeness4/5

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

Given the output schema, annotations, and input schema, the description covers the essential purpose, input locality, and installation prerequisite. It leaves sibling routing and detailed parameter semantics to structured fields, which is reasonable, though a brief note on when to prefer it over search_amr_genes would improve completeness.

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 67%: fasta_path and organism are documented in the schema, while sequence_type is an enum without its own description. The phrase "genome or proteome" lightly maps to nucleotide/protein input, but the description otherwise adds little parameter-level meaning beyond the schema.

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?

The description uses a specific verb and resource: "Screen a local genome or proteome for AMR genes" and names AMRFinderPlus. It implicitly distinguishes this local screening tool from database-search siblings by emphasizing "local" and local installation, though it does not explicitly name an alternative.

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?

It provides a clear prerequisite ("must be installed locally") and implies use for local genome/proteome files, but it gives no explicit when-to-use guidance versus siblings such as search_amr_genes. It also states no exclusions or conditions under which this tool should not be used.

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

Deploy Server