Skip to main content
Glama
systemsomicslab

ms-data-parser

console_method_template

Idempotent

Creates a method file for the opposite polarity by replacing ion mode and searched adduct ions while keeping detection and alignment settings. Use when one polarity has never been processed in the GUI.

Instructions

既存のパラメータから、別極性用のメソッドファイルを作ります(最後の手段)。

まず console_plan の method_file 省略を試してください。 MS-DIAL GUI は解析の たびに <project>_param_<終了時刻>.txt を自動保存するので、その極性で一度でも GUI 実行があれば、作る必要はありません。

このツールが要るのは「その極性で一度も処理していない」場合だけです (別極性は処理済み、というのが典型)。やることは 2 行の差し替えです: Ion mode と Searched adduct ions をその極性の標準セットにする。 検出・アライメント条件は元のまま引き継ぎます(勝手に変えると別の解析になる)。 加えて、GUI 由来では必ず空の Lbm file path を解決して埋めます。

out_path: 書き出し先。 polarity: "positive" / "negative"(作りたい側)。 based_on: 元にするパラメータファイル。省略時は dataset_root から探します (極性は問いません — 別極性から作るのがこのツールの用途なので)。 dataset_root: based_on 省略時の探索先。dataset_root 直下・兄弟フォルダ・ 過去 run まで探します。候補が複数あれば based_on で選ぶよう METHOD_FILE_CHOICE_REQUIRED で止まります(土台の選択は解析条件そのもの なので、最新を黙って採りません)。 library_mode: "auto"(既定)か "msp_only"。"msp_only" は console_plan と同じく Lbm file path を空にし、Msp file path に作りたい極性の研究室 MSP を書き、 Text DB と注釈器設定表の宣言を空にする(解決順・止まる条件も console_plan と同じ)。 msp_file: library_mode="msp_only" で使う MSP の明示パス。

Input Schema

NameRequiredDescriptionDefault
omicsNolipidomics
based_onNo
msp_fileNo
out_pathYes
polarityYes
dataset_rootNo
library_modeNoauto

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.7/5.0
Behavior5/5

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

Annotations already mark it as non-destructive, idempotent, and not read-only, and the description goes well beyond that: it states that detection/alignment conditions are inherited unchanged, that the empty `Lbm file path` is always resolved, that ambiguous candidates halt with `METHOD_FILE_CHOICE_REQUIRED` rather than silently picking the newest, and how `library_mode=msp_only` rewrites library paths. That is exactly the operational context annotations cannot carry.

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 critical guidance (try console_plan first) is front-loaded before any parameter detail, and each paragraph maps to a decision the caller must make. It is on the long side with heavy bold emphasis, but for a 7-parameter tool with zero schema descriptions every sentence does real work; only minor tightening is possible.

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?

For a 7-parameter mutation tool with no output schema, the description covers purpose, prerequisites, exact mutation surface, stop conditions, and mode behavior. Remaining gaps are small: what the call returns (a path? a confirmation?) is not stated, and the `omics` parameter is undocumented.

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?

With 0% schema description coverage the description carries the full burden, and it does so for six of seven parameters: `polarity` values ('positive'/'negative'), `based_on` being polarity-agnostic, `dataset_root` search scope, `library_mode` values and their effect, and `msp_file` usage. The `omics` parameter (default 'lipidomics') is never mentioned, leaving one gap in an otherwise thorough mapping.

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 opens with a specific verb and resource (creates a method/parameter file for the opposite polarity from existing parameters) and immediately distinguishes this from the sibling tool console_plan by framing itself as a last resort. It also scopes the change precisely (only `Ion mode` and `Searched adduct ions` are swapped), which tells an agent exactly what artifact it produces.

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?

It gives an explicit when-not ('まず console_plan の method_file 省略を試してください') with the reason (the GUI auto-saves `<project>_param_<終了時刻>.txt` on every run), and an explicit when ('その極性で一度も処理していない場合だけ'). The alternative and the decision rule that selects it are both named, so no inference is required.

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