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ms-data-parser

console_prepare_input

Idempotent

Creates a single-format input folder from raw MS data by keeping only the chosen acquisition files and their companion files, resolving mixed-format errors while leaving the source folder unchanged.

Instructions

計測フォーマットが 1 種類だけの入力フォルダを作ります(MIXED_RAW_FORMATS の解消)。

MS-DIAL は .wiff と .wiff2 を別フォーマットとして数えるため、SCIEX の 生データフォルダはそのままでは対話プロンプトが出て実行できません。 このツールは指定した拡張子の計測ファイルとその随伴ファイル (.wiff.scan / .timeseries.data 等)だけを集めたフォルダを作ります。

Agilent・Bruker の .d と Waters の .raw のようにフォルダそのものが 1 検体の形式も扱えます。その場合はフォルダ構造を実体として作り直し、 中のファイルだけをリンクします(フォルダ自体はリンクにしません)。

実体はコピーせずハードリンクを張ります(同一ボリュームで無い場合のみコピー)。 元フォルダは一切変更しません。 MS-DIAL の生成物はこの新しいフォルダ側に 出るので、生データ本体を汚さずに済みます。

dataset_root: 生データフォルダ。 keep_extension: 残す計測拡張子(既定 "wiff")。MS-DIAL が読む 12 形式 (abf / ibf / cdf / mzml / wiff / raw / d / wiff2 / qgd / lcd / lrp / imzml)から選びます。MIXED_RAW_FORMATS の formats が実際の内訳です。 out_dir: 出力先。省略時は <元フォルダ>_<拡張子> を兄弟として作ります。

Input Schema

NameRequiredDescriptionDefault
out_dirNo
dataset_rootYes
keep_extensionNowiff

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.6/5.0
Behavior5/5

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

Rich disclosure beyond the annotations: hard links instead of copies, copies only when the volumes differ, the source folder is never modified (consistent with destructiveHint=false), and MS-DIAL outputs land in the new folder. It also explains that for .d/.raw-style formats the directory tree is recreated and only inner files are linked, which an agent could not infer from any structured field.

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 purpose and the motivating failure mode are front-loaded, followed by behavior and then a parameter glossary, which is a sensible order. It is on the long side with some explanatory redundancy about the wiff/wiff2 distinction, but every block is functional.

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 two-hint, no-output-schema tool the description is nearly complete: it covers behavior, safety, defaults, and valid inputs. The one gap is the return value (the created path / summary) and idempotency behavior on re-run with an existing out_dir, which is not spelled out.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must carry all parameter meaning — and it does: dataset_root is the raw folder, keep_extension defaults to "wiff" and enumerates the 12 MS-DIAL-readable extensions, and out_dir defaults to the sibling <source>_<extension>. This is exactly the value the schema lacks.

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?

It pairs a concrete verb (create a folder holding one measurement format) with the exact problem state it resolves (MS-DIAL's MIXED_RAW_FORMATS prompt / SCIEX .wiff vs .wiff2). No sibling tool addresses this remediation step, so the purpose is distinguishable without opening the schema.

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?

It states the trigger condition clearly — a raw folder that would otherwise raise MIXED_RAW_FORMATS and prompt interactively — and describes handling of folder-as-sample formats (.d, .raw). It does not name exclusions or an alternative tool (e.g. console_cleanup / console_plan) when this is not the right step, so it stops short of a 5.

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