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export_code

Generates standalone reproduction code for metabolite mapping using original library APIs, outputting a Python script and Jupyter notebook for full reproducibility.

Instructions

Write standalone reproduction code that reproduces the run using the ORIGINAL library APIs (MetaboAnalystR/BridgeDbR/KEGGREST via Rscript, PubChem PUG-REST, molmass, COBRApy, matplotlib) — NOT the tool wrappers. Emits both code/reproduce_mapping.py (flow-based, reads the saved ledger) and code/reproduce_mapping.ipynb (same flow unrolled into linear cells, no def, with detailed input/output/reuse comments per cell).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
workdirYes
Behavior4/5

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

No annotations are provided, so the description carries the full burden. It details the output: two code files with specific formats. It does not mention side effects, permissions, or rate limits, but as an export tool, it is likely non-destructive and does not modify state. The description provides sufficient behavioral context for safe invocation.

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 a single paragraph but is well-structured, starting with the main action. It is detailed yet efficient, with no redundant sentences. However, it could be broken into shorter sentences for easier parsing.

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

Completeness4/5

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

Given only one parameter and no output schema, the description adequately covers the tool's purpose and output. It explains what files are generated and their format. It could mention prerequisites like a completed run or required directories, but overall it is sufficiently complete for an export tool.

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?

Only one parameter, 'workdir', is in the schema with no description (0% coverage). The tool description does not explain what 'workdir' represents or its expected format. With low schema coverage, the description should compensate but fails to add meaning beyond the parameter name.

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 the tool's purpose: writing standalone reproduction code using original library APIs. It specifies the verb 'write', the resource 'reproduction code', and details the libraries and output files. It distinguishes from sibling tools by focusing on code export rather than data lookup or plotting.

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 does not explicitly state when to use this tool versus alternatives. It implies usage after a run for reproducibility, but lacks explicit 'when to use' or 'when not to use' guidance. Sibling tool names suggest other functions, but no comparative advice is given.

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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