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write_tool

Save AnnData objects to file with configurable formats and compression for single-cell RNA sequencing analysis workflows.

Instructions

Write AnnData objects to file.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
filenameYesPath to save the file. If no extension is provided, the default format will be used.
extNoFile extension to infer file format. If None, defaults to scanpy's settings.file_format_data.
compressionNoCompression format for h5 files.gzip
compression_optsNoCompression options for h5 files.
Behavior2/5

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

With no annotations provided, the description carries full burden but only states the basic function. It doesn't disclose whether this is a destructive operation (overwrites existing files), what permissions are needed, error conditions, or what happens upon success. The description lacks behavioral context beyond the minimal action statement.

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?

The description is a single, direct sentence with zero wasted words. It's perfectly front-loaded with the core action and immediately communicates the essential function without any fluff or unnecessary elaboration.

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?

For a write operation with 4 parameters and no annotations or output schema, the description is inadequate. It doesn't explain what AnnData objects are, what formats are supported beyond what's in the schema, whether the operation is atomic, what validation occurs, or what happens on failure. The context demands more complete guidance for a file-writing tool.

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 description coverage is 100%, so the schema already documents all parameters thoroughly. The description adds no parameter information beyond what's in the schema, maintaining the baseline score of 3. It doesn't explain relationships between parameters (e.g., how 'ext' interacts with 'filename' extension).

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 action ('Write') and the resource ('AnnData objects to file'), making the purpose immediately understandable. However, it doesn't differentiate from sibling tools like 'read_tool' beyond the obvious directionality, nor does it specify what AnnData objects are in this context.

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 is provided about when to use this tool versus alternatives. While 'read_tool' is clearly the complementary operation, there's no mention of prerequisites (e.g., needing an AnnData object in memory), file format considerations, or when other tools might be more appropriate for data export.

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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