Skip to main content
Glama
systemsomicslab

ms-data-parser

eic_plot_chromatograms

Read-only

Return structured, client-neutral JSON plot data for selected EIC chromatograms, enabling MCP clients or LLMs to render sample traces without generating images or files.

Instructions

Return client-neutral plot data for selected EIC chromatograms.

This read-only tool returns structured lipidmix.eic.v1 JSON only. It does not render an image and does not write files: Use-LLLM may render the series with Plotly, while Claude Desktop or another MCP client may use its own UI. Call save_figure(kind="eic") only after the user explicitly requests PNG output.

spot_id is exact and should normally come from the existing m/z or RT search tools. file_ids selects at most 12 sample traces; when omitted all traces are returned only if the spot contains 12 samples or fewer.

Input Schema

NameRequiredDescriptionDefault
titleNo
spot_idYes
file_idsNo
file_pathNo
normalizeNonone

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A3.9/5.0
Behavior4/5

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

The description adds useful behavior beyond readOnlyHint=true: it returns only structured lipidmix.eic.v1 JSON, does not render images or write files, and is client-neutral. It also states a 12-trace limit for file_ids. It does not fully explain the returned JSON shape or several parameters.

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 front-loaded with the purpose and then adds constraints in a compact, readable way. Every sentence contributes useful routing or behavioral information without unnecessary repetition.

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?

For a read-only plotting-data tool with no output schema and low parameter description coverage, the description does well to explain output format and file behavior. However, it omits meaning for title, file_path, and especially normalize, and does not describe the structured JSON content enough for an agent to fully anticipate the response.

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

Parameters2/5

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 parameter meaning. It explains spot_id as exact and sourced from search tools, and file_ids as selecting at most 12 traces, but it does not explain title, file_path, or normalize, leaving three of five parameters undocumented.

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 states a specific verb and resource: return client-neutral plot data for selected EIC chromatograms. It clearly distinguishes this from image rendering and save_figure, but does not explicitly differentiate it from the sibling eic_plot_compounds tool.

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 explicit usage guidance: use for structured EIC plot data, do not use for rendering or writing files, and call save_figure(kind="eic") only after an explicit PNG request. It also says spot_id normally comes from existing m/z or RT search tools and explains file_ids selection behavior.

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