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systemsomicslab

ms-data-parser

dcl_parser

Read-only

Parse a single MS-DIAL .dcl result to summarize MS/MS peak inventory, acquisition rate, and precursor ranges, returning a short preview of main fragments for downstream lipidomics review.

Instructions

1つの .dcl(MSDecResult)を解析し、MS/MS 在庫の要約と先頭数件を返す。

.dcl は測定ファイル1つにつき1個で、dcl_index が同名 .pai2 のピーク順に 対応する。返すのは取得率・ピーク本数分布・precursor m/z / RT 範囲の要約と、 先頭 preview 件の主要フラグメント。個々のピークの同定確度に効かせるには pai2_parser(同名 .dcl を自動で付与する)→ verify_peak_annotation を使う。

  • top_n_peaks: 各スペクトルを強度上位 N 本に間引く(既定 10。全件は 0 を指定)。

  • preview: 要約に添える MSDecResult の件数。

Input Schema

NameRequiredDescriptionDefault
previewNo
file_pathNo
top_n_peaksNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.3/5.0
Behavior4/5

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

With readOnlyHint=true already covering safety, the description adds real context: one `.dcl` per measurement file, `dcl_index` matches peak order in the same-named `.pai2`, and what the summary contains (acquisition rate, peak-count distribution, precursor m/z and RT ranges). It doesn't discuss file-size limits or failure behavior, so it stops short of 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?

The opening sentence states purpose and return value up front, then context, routing, and a bulleted parameter list. Dense and mostly waste-free, though the parameter bullets and the prose overlap slightly.

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?

No output schema exists, so the description correctly describes the return shape (summary statistics + preview entries). The main omission is how `file_path` is resolved when it is null, which matters for a file-taking tool.

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 coverage is 0%, so the description must carry the parameters, and it explains two of them well: `top_n_peaks` (default 10, 0 = keep all) and `preview` (number of MSDecResults appended to the summary). `file_path`, which is nullable, is not explained at all, leaving one gap.

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?

States a specific verb and resource: parses a single `.dcl` (MSDecResult) and returns an MS/MS inventory summary plus the first few entries. It also names the sibling (`pai2_parser`) used for a different purpose, so an agent can tell the two apart without opening schemas.

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

Usage Guidelines4/5

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

Explicitly routes the agent: for per-peak identification confidence, use `pai2_parser` → `verify_peak_annotation`. That gives a clear alternative and condition. It lacks an explicit 'do not use this when…' statement, but the positive routing is strong.

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