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analyze_velocity_data

Analyze RNA velocity from single-cell data with spliced and unspliced layers to infer cellular dynamics and fate transitions.

Instructions

Analyze RNA velocity to understand cellular dynamics. Requires 'spliced' and 'unspliced' layers.

Args:
    data_id: Dataset ID
    params: Velocity parameters (method, scvelo_mode, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
data_idYes
paramsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
data_idYes
velocity_computedYes
velocity_graph_keyNo
modeYes
Behavior2/5

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

Annotations are not informative (readOnlyHint=false, etc.), so the description carries the burden. It only states a requirement but does not disclose what the tool does to the data, whether it modifies state, or what output to expect. This is insufficient for a tool performing RNA velocity analysis.

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?

The description is very short and front-loaded, which is good for quick understanding. The 'Args' section is clear, though it could be integrated better. Every sentence earns its place, but the description could be slightly more structured.

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 tool (many parameters, no output schema provided), the description is incomplete. It fails to mention the output or what happens after analysis. The requirement for specific layers is good, but overall it lacks depth for a tool with such detailed parameters.

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 adds minimal value beyond the input schema. It lists data_id and params but only gives a shallow idea of params. The inner schema has more detail (enums, defaults) but is not referenced. Schema coverage is 0% at top level, so the description should compensate, but it barely does.

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 'RNA velocity', and mentions it is for understanding cellular dynamics. It distinguishes from siblings like 'analyze_trajectory_data' but does not explicitly differentiate, so a 4 is appropriate.

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

Usage Guidelines3/5

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

The description mentions that 'Requires spliced and unspliced layers' provides a precondition, which gives some context on when to use the tool. However, it does not provide guidance on when to use this tool versus alternatives like analyze_trajectory_data or compute_embeddings, so a 3 for implied usage.

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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