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find_spatial_genes

Idempotent

Identify genes with spatial expression patterns in spatial transcriptomics data, selecting from methods like FlashS, SPARKX, or SpatialDE with adjustable parameters.

Instructions

Identify spatially variable genes.

Args:
    data_id: Dataset ID
    params: Spatial variable gene parameters (method, n_top_genes, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paramsNo
data_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
methodYes
data_idYes
p_valuesNo
q_valuesNo
results_keyYes
spatial_genesYes
flashs_resultsNo
sparkx_resultsNo
gene_statisticsNo
n_genes_analyzedYes
spatialde_resultsNo
n_significant_genesYes
Behavior2/5

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

Annotations indicate idempotentHint=true and readOnlyHint=false, but the description does not clarify that the tool modifies data or saves results. It simply says 'identify', which is ambiguous. No added behavioral details.

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?

Very concise (two sentences) with clear 'Args' structure. However, it could be more informative without losing brevity.

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?

Given the complexity of the params object and the existence of an output schema, the description is too brief. It does not explain what the tool returns or any side effects, leaving gaps for an agent.

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?

The description mentions 'data_id' and 'params' with brief hints, but the nested params object has extensive schema descriptions. However, the tool description covers only 0% of these sub-parameters, and the 'etc.' lacks specificity. Schema coverage is high but the description itself adds minimal value.

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?

Clearly states 'Identify spatially variable genes' with a specific verb and resource, but does not differentiate from sibling tools like analyze_spatial_statistics.

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?

No guidance on when to use this tool versus alternatives, nor any when-not-to-use conditions. Only lists arguments without 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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