skills/tooluniverse-custom-tool/SKILL.md
Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.
npx skillsauth add mims-harvard/tooluniverse tooluniverse-custom-toolInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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When to create a custom tool: Create one if you need to access an API that ToolUniverse doesn't cover, or if you need a specialized data transformation that no existing tool provides. Start with the JSON config approach (simplest — no Python needed); escalate to a Python class only if you need custom response parsing or stateful logic.
Three ways to add tools — pick the one that fits your needs:
| Approach | When to use | |---|---| | JSON config | REST API with standard request/response — no coding needed | | Python class (workspace) | Custom logic for local/private use only | | Plugin package | Reusable tools you want to share or install via pip |
Tools in .tooluniverse/tools/ are auto-discovered at startup. No installation needed.
mkdir -p .tooluniverse/tools
Create .tooluniverse/tools/my_tools.json:
[
{
"name": "MyAPI_search",
"description": "Search my internal database. Returns matching records with id, title, and score.",
"type": "BaseRESTTool",
"fields": {
"endpoint": "https://my-api.example.com/search"
},
"parameter": {
"type": "object",
"properties": {
"q": {
"type": "string",
"description": "Search query"
},
"limit": {
"type": ["integer", "null"],
"description": "Max results to return (default 10)"
}
},
"required": ["q"]
}
}
]
One JSON file can define multiple tools — just add more objects to the array.
For the full JSON field reference, see references/json-tool.md.
Create .tooluniverse/tools/my_tool.py:
from tooluniverse.tool_registry import register_tool
@register_tool
class MyAPI_search:
name = "MyAPI_search"
description = "Search my internal database. Returns matching records with id, title, and score."
input_schema = {
"type": "object",
"properties": {
"q": {"type": "string", "description": "Search query"},
"limit": {"type": "integer", "description": "Max results (default 10)"}
},
"required": ["q"]
}
def run(self, q: str, limit: int = 10) -> dict:
import requests
resp = requests.get(
"https://my-api.example.com/search",
params={"q": q, "limit": limit},
timeout=30,
)
resp.raise_for_status()
return {"status": "success", "data": resp.json()}
Note: workspace Python tools use run(self, **named_params) — arguments are unpacked as keyword
arguments matching the input_schema properties.
For the full Python class reference, see references/python-tool.md.
# Uses test_examples from the tool's JSON config — zero config needed
tu test MyAPI_search
# Single ad-hoc call
tu test MyAPI_search '{"q": "test"}'
# Full config with assertions
tu test --config my_tool_tests.json
tu test automatically runs these checks on every call:
return_schema validation — validates result["data"] against the JSON Schema defined in return_schema (if present)expect_status and expect_keys — only if set in the config fileGotchas: (1) tu test does NOT verify non-empty results — [] passes schema validation. Use test_examples args that return real data. (2) Verify test_examples manually first with urllib (not curl) to confirm the API returns JSON, not HTML. Use 2-4 broad keywords.
Add test_examples and return_schema to JSON config for best coverage. tu test validates result["data"] against return_schema (match "type": "array" or "type": "object" to your data shape).
Optional my_tool_tests.json for extra assertions (expect_status, expect_keys).
Tools in .tooluniverse/tools/ are auto-available via tu serve. Workspace priority: --workspace flag → TOOLUNIVERSE_HOME env → ./.tooluniverse/ → ~/.tooluniverse/.
To use a different tools directory, add sources: [./my-custom-tools/] in .tooluniverse/profile.yaml and start with tooluniverse --load .tooluniverse/profile.yaml.
Use this when you want to distribute tools as a reusable Python package that other users can
install with pip install. The plugin package has the same directory layout as a workspace, plus a
pyproject.toml that declares the entry point.
my_project_root/ # directory containing pyproject.toml
pyproject.toml
my_tools_package/ # importable Python package (matches entry-point value)
__init__.py # minimal — one-line docstring, no registration code
my_api_tool.py # tool class(es) with @register_tool
data/
my_api_tools.json # JSON tool configs (type must match registered class name)
profile.yaml # optional: name, description, required_env
JSON config files are discovered from both data/ and the package root directory. The convention is data/.
pyproject.toml entry point[project.entry-points."tooluniverse.plugins"]
my-tools = "my_tools_package"
The value (my_tools_package) must be the importable Python package name.
Plugin package tools use BaseTool and receive all arguments as a single Dict:
import requests
from typing import Dict, Any
from tooluniverse.base_tool import BaseTool
from tooluniverse.tool_registry import register_tool
@register_tool("MyAPITool")
class MyAPITool(BaseTool):
"""Tool description here."""
def __init__(self, tool_config: Dict[str, Any]):
super().__init__(tool_config)
self.timeout = tool_config.get("timeout", 30)
fields = tool_config.get("fields", {})
self.operation = fields.get("operation", "search")
def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
query = arguments.get("query", "")
if not query:
return {"error": "query parameter is required"}
try:
resp = requests.get(
"https://my-api.example.com/search",
params={"q": query},
timeout=self.timeout,
)
resp.raise_for_status()
return {"status": "success", "data": resp.json()}
except requests.exceptions.RequestException as e:
return {"error": str(e)}
Key differences from the workspace pattern:
BaseTool (from tooluniverse.base_tool)@register_tool("ClassName") takes the class name as a string argumentrun(self, arguments: Dict) receives all arguments in a single dict — extract them with .get()__init__ receives tool_config dict; call super().__init__(tool_config) firstPlace configs in data/my_api_tools.json. The "type" field must match the string passed to
@register_tool(...):
[
{
"name": "MyAPI_search",
"description": "Search my API. Returns matching records.",
"type": "MyAPITool",
"fields": { "operation": "search" },
"parameter": {
"type": "object",
"properties": {
"query": { "type": "string", "description": "Search query" },
"limit": { "type": ["integer", "null"], "description": "Max results" }
},
"required": ["query"]
}
}
]
__init__.pyKeep minimal — just a docstring. The plugin system auto-imports all .py files via _discover_entry_point_plugins(), so @register_tool decorators fire automatically. Optional: add from . import my_api_tool for IDE support (idempotent). Do NOT add registration logic or JSON loading here.
pip install -e /path/to/my_project_root
cd /path/to/my_project_root # MUST run from plugin repo directory
tu test MyAPI_search '{"query": "test"}'
Must pip install -e first. Run tu test from plugin repo dir (workspace auto-detection needs .tooluniverse/). Add test_examples to JSON config for zero-config testing. Use tu info MyAPI_search to confirm the tool loaded.
Calculator tools (no HTTP) follow the plugin-package pattern but skip the HTTP layer. Key design patterns:
Dict[str, float] at module level. Resolution priority: explicit value → preset name → default. Include presets in metadata for discoverability.operation values in a single tool. Use "fields": {"operation": "default_op"} in JSON config._MU0 = 4*pi*1e-7, etc.). Material-specific values as named dicts.data (e.g., temperature + headroom + pass/fail) rather than forcing multiple calls.For complete patterns, see references/python-tool.md.
tools
Post-market safety surveillance and recall/adverse-event RETRIEVAL across the full spectrum of FDA-regulated products that are NOT covered by the drug-AE signal skills: medical devices, food / dietary supplements / cosmetics, veterinary drugs, and drug supply (shortages). Orchestrates openFDA endpoints (MAUDE device adverse events + device recalls + 510(k), CAERS food/supplement/ cosmetic adverse events, veterinary adverse events, drug shortages, and cross-product enforcement/recall reports). USE WHEN the user asks: "are there adverse events for [device / pacemaker / infusion pump / insulin pump]", "device recalls for [firm/product]", "supplement / vitamin / cosmetic adverse reactions", "is [drug] in shortage", "what injectables are on shortage", "veterinary / animal adverse events for [drug] in [dog/cat/horse]", "food recall for listeria", "MAUDE report for [device]", "CAERS reactions for [brand]". DO NOT USE for drug adverse-event SIGNAL detection or disproportionality (PRR / ROR / IC) or drug-AE association scoring — that is `tooluniverse-pharmacovigilance` / `tooluniverse-adverse-event-detection`. This skill is multi-product surveillance and retrieval, not drug-AE statistical signal mining.
tools
--- name: tooluniverse-phewas description: Cross-ancestry / cross-biobank phenome-wide association (PheWAS) and replication. Given ONE variant (rsID) or ONE gene, look up every phenotype it associates with across European/UK (UKB-TOPMed), Finnish (FinnGen), Japanese (BioBank Japan), and Taiwanese (TPMI) biobanks, plus exome-wide gene-burden PheWAS (Genebass), then judge whether an association replicates across ancestries or is population-specific. Use whenever the user asks "what else is this va
tools
Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
tools
Genome-ASSEMBLY discovery, QC, and replicon mapping for any organism (bacteria, archaea, fungi, and beyond) using NCBI Datasets. Resolves an organism name or taxid to assemblies, picks the reference/representative or best-quality assembly, pulls assembly QC metrics (total length, contig/scaffold N50, contig count, GC%, assembly level, RefSeq category), enumerates chromosomes and plasmids via per-replicon sequence reports, and compares candidate assemblies on quality. Use for "what genomes are available for [organism]", "assembly stats / N50 / GC content for [GCF_/GCA_ accession]", "how many plasmids does [strain] have", "compare assemblies for [species]", "find the reference genome for [taxon]", "is this assembly Complete Genome or just contigs". NOT for gene-level orthology/synteny (use tooluniverse-comparative-genomics), plant gene structure (use tooluniverse-plant-genomics), de novo assembly from raw reads (no tool exists), or taxonomy-only name/lineage lookups.