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Analyze Lcms Series

analyze_lcms_series

Parse a chronological series of LCMS PDF reports to identify trends in mass and retention time changes across samples.

Instructions

Analyze a chronological series of standard LCMS PDF reports.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
filesYes
output_pathNo
mz_toleranceNo
rt_toleranceNo
trend_thresholdNo
ignore_instrumentNo
Behavior1/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It fails to mention what 'analyze' entails—whether it produces a summary, modifies files, requires specific permissions, or any side effects. The phrase 'chronological series' hints at ordering but does not describe the analysis logic or output format. This is a significant gap for a non-trivial tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness2/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single sentence, which is technically concise, but it is significantly under-specified rather than appropriately concise. It lacks necessary details about the tool's behavior and parameters, making it more a placeholder than a well-structured definition. The sentence is front-loaded with the verb, but that cannot compensate for the missing substance.

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

Completeness1/5

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

Given the tool's complexity (6 parameters, no annotations, no output schema), the description is woefully incomplete. It does not explain the analysis workflow, expected inputs, output format, or how parameters influence behavior. An agent would have no idea what to expect or how to invoke this tool correctly beyond providing a list of files.

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

Parameters1/5

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

Schema description coverage is 0%, so the description must compensate for the six parameters. It mentions 'standard LCMS PDF reports' but does not clarify the purpose of 'files', 'output_path', 'mz_tolerance', 'rt_tolerance', 'trend_threshold', or 'ignore_instrument'. Without any parameter explanation, agents cannot infer correct usage from the description alone.

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 clearly states the verb 'Analyze' and the resource 'a chronological series of standard LCMS PDF reports'. This is specific enough to distinguish it from generic parsing tools, though it does not name an explicit alternative or sibling. The purpose is understandable but not fully differentiated from similar tools like parse_analysis_file or discover_experiment_files.

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?

The description offers no guidance on when to use this tool versus alternatives, no prerequisites, no exclusions, and no context about the intended workflow. It merely states what it does without indicating scenarios where it is preferred or where another tool (e.g., parse_analysis_file for single files) would be more appropriate.

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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