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create_qq_plot

Generate a Quantile-Quantile (QQ) plot from GWAS p-values to compare observed vs expected distributions, assessing inflation or bias in summary statistics.

Instructions

Create a Quantile-Quantile (QQ) plot from GWAS p-values. Shows observed vs expected p-values.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sumstats_pathYesPath to GWAS summary statistics file
output_pathNoPath to save the plot
titleNoPlot titleQQ Plot
Behavior2/5

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

No annotations are provided, so the description must cover behavioral traits. It only states it 'creates a plot' and 'shows observed vs expected p-values', but does not disclose file format requirements, computational cost, or whether it is a read-only operation.

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?

Two sentences with no unnecessary words. The action verb and subject are front-loaded. Every word is meaningful.

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?

Given the simplicity of the tool (3 params, no output schema, no annotations), the description is adequate but not complete. It does not specify expected input file format or what happens with the output file.

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

Parameters3/5

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

Schema coverage is 100%, so baseline is 3. The description adds context ('from GWAS p-values') but does not provide additional meaning beyond the parameter names and descriptions already in the schema.

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 clearly states 'Create a Quantile-Quantile (QQ) plot from GWAS p-values', specifying the tool's verb, resource, and purpose. It distinguishes itself from siblings like 'create_manhattan_plot' by mentioning QQ plots and p-values.

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?

The description indicates when to use: when you have GWAS p-values. However, it does not explicitly state when not to use or provide alternatives, though the sibling list is available for context.

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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