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annotate_source

Append metabolite identifiers (KEGG, HMDB, ChEBI, PubChem, InChIKey) to the original intensity matrix by matching compound names, creating annotated .xlsx and .tsv files.

Instructions

Append the final ID-result columns to the ORIGINAL data file — the intensity matrix keeps all its columns and gains ID_final_class / ID_confidence / ID_kegg / ID_hmdb / ID_chebi / ID_pubchem / ID_inchikey / ID_gem_mam per compound (matched by name).

Uses the source recorded by ingest_names if source is omitted. header is the 0-based header row (some vendor sheets have a preamble row, e.g. header=1). Writes _annotated .xlsx + .tsv into the workdir.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
outNo
sheetNo
headerNo
sourceNo
workdirYes
name_columnNo
Behavior3/5

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

With no annotations, the description must fully disclose behavior. It describes the appending action, that the original file's columns are kept, and that outputs are written to the workdir. However, it does not explicitly state that the original file is not modified, and it lacks details on permissions, rate limits, or potential side effects. The description adds some context but could be more thorough.

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 reasonably concise, with the primary action front-loaded in the first sentence. The second paragraph adds key parameter details without redundancy. While some information is repeated between schema and description, the text is efficient and clear.

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 6 parameters, 0% schema coverage, no output schema, and no annotations, the description covers the core workflow but misses some parameter meanings (out, sheet, name_column). It explains output files and columns added, but lacks details on return values or side effects. It is adequate but not fully complete for a complex 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 coverage is 0%, so the description must explain parameters. It explains 'source' (defaulting to ingest_names record) and 'header' (0-based row index for preamble), but does not cover 'out', 'sheet', or 'name_column'. This leaves 3 out of 6 parameters undocumented in the description, providing only partial compensation for the schema gap.

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 tool appends ID columns to the original data file and lists the specific columns added. It explains the matching by compound name and outputs. However, it does not differentiate from sibling tools like exact_match or verify_candidate, leaving some ambiguity about when to use this tool over others.

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?

The description provides minimal guidance on when to use this tool. It mentions that if 'source' is omitted, it uses the source recorded by ingest_names, and explains the header parameter. But there is no explicit instruction on when to use this tool versus alternatives, nor any exclusions or prerequisites.

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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