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CovaSyn Chemistry Tools

covams_process_spectrum

Pre-process an MS spectrum (smoothing, peak picking, deisotoping, normalization).

Input Schema

NameRequiredDescriptionDefault
peaksYes
stepsNo
paramsNo
api_keyNo

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

C2.7/5.0
Behavior2/5

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

No annotations are supplied, so the description carries the full behavioral burden, yet it only lists operation names. It does not disclose whether preprocessing mutates the input peaks, whether the steps run in a fixed or specified order, that an api_key parameter implies authentication, or any rate-limit/error behavior.

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?

A single tight sentence with the verb and resource front-loaded and zero filler. It is appropriately sized, though its brevity reflects under-specification rather than genuine conciseness.

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

Completeness2/5

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

An output schema exists, so return values need not be described, but the tool has 4 undocumented parameters, no annotations, and no usage guidance. For a non-trivial preprocessing tool, the description is far too thin to let an agent call it correctly.

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% for 4 parameters, so the description must compensate. The parenthetical 'smoothing, peak picking, deisotoping, normalization' loosely hints at the values for `steps`, but `peaks` format, the `params` object contents, and `api_key` are entirely unexplained in both schema and description.

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?

States a specific verb ('Pre-process') and resource ('MS spectrum') and even enumerates the sub-operations, so the agent knows exactly what the tool does. However, it gives no differentiation from adjacent siblings like covams_detect_features or covams_spectral_quality, which an agent could easily confuse with a preprocessing step.

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

Usage Guidelines2/5

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

There is no when-to-use, when-not-to-use, or alternative-tool guidance. The only clue is the implicit role of preprocessing in an MS pipeline, which the agent must infer. Among dozens of covams siblings, no routing information is provided.

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

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