What is implement-tool?

A guided workflow for adding a new bioinformatics tool wrapper to the proto-tools project. A wrapper connects the project to an external program used to process biological data.

It helps research the external tool, define its input and output contract, implement the wrapper, test real temporary workloads, audit configuration fields, verify documentation and licenses, and prepare the change for release.

It breaks the work into research, implementation, parallel review, testing, documentation checks, and final review so important integration problems are less likely to be missed.

How evo-design/proto-tools configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to evo-design/proto-tools. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/evo-design/proto-tools/main/.claude/skills/implement-tool/SKILL.md

Clone the repo

git clone --depth 1 https://github.com/evo-design/proto-tools

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/evo-design/proto-tools/implement-tool/github.svg)](https://agentmods.dev/skills/evo-design/proto-tools/implement-tool)

Your own site

<a href="https://agentmods.dev/skills/evo-design/proto-tools/implement-tool"><img src="https://agentmods.dev/badge/skills/evo-design/proto-tools/implement-tool/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/evo-design/proto-tools/implement-tool"><img src="https://agentmods.dev/badge/skills/evo-design/proto-tools/implement-tool.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 93 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 15,148 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00093	$0.15148
Opus 5.5	$0.00037	$0.06059
Sonnet 5.5	$0.00019	$0.03030
Haiku 4.5	$0.00009	$0.01515

Measured 6d ago against content hash 72fbca16721e, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

implement-tool scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

wget -q -O "$WEIGHTS_DIR/model.pt" "https://example.com/model.pt"

.claude/skills/implement-tool/SKILL.md · 1,022 lines

How it starts

The opening of the file, as written. The whole thing — 1,022 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Implement a New Tool — Orchestrator Pipeline

You are implementing a new bioinformatics tool in the proto-tools codebase. This skill orchestrates the full lifecycle using parallel subagents for speed.

Pipeline overview:

Phase 1: Research → Phase 2: Contract → Phase 3: Fan-out (5 parallel agents) → Phase 4: Verify → Phase 4.5: Config Field Audit → Phase 4.6: Temp Integration & Stress → Phase 4.7: Docs Verification → Phase 4.8: Self-Audit & Full PR Review → Phase 5: Ship

The Phase 4.x gates are decisive and non-negotiable — they catch the failure modes that the fast fan-out reliably misses (invented config parameters, untested real workloads, hallucinated citations/licenses, missing license.yaml/links.yaml). Do not skip them to ship faster. Ground every decision in upstream source or a credible reference — never assume.

Key principle: The core tool file (Input/Config/Output + @tool() + run_*()) is the contract everything else depends on. Write it first (sequential), then fan out to subagents (parallel).

CRITICAL: Standalone scripts run in isolated environments and MUST NOT import from proto_tools:

from proto_tools.utils import ... — will fail at runtime
from proto_tools.entities import ... — will fail at runtime
from standalone_helpers import get_subprocess_device_env — published on PYTHONPATH (OK)
Standard library imports: import json, import subprocess, etc. (OK)
Dependencies from requirements.txt: import torch, import numpy, etc. (OK)
NEVER install proto_tools in standalone environments (creates circular dependency, breaks isolation)

Phase 0: Parse Input

The user provides EITHER:

A GitHub issue URL/number (e.g., #<issue-number> or https://github.com/evo-design/proto-tools/issues/<issue-number>)
A tool name + source repo (e.g., "ESM-IF from https://github.com/facebookresearch/esm")

If a GitHub issue is provided:

Fetch the issue with gh issue view <number> --json title,body,labels
Extract from the issue body: tool name, source repo URLs, paper links, category, operations
Present the extracted info to the user for confirmation

Read the full file on GitHub · 1,022 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

6d ago Changed · +26 lines 72fbca16721e
11d ago Changed 47e7052d3d0f
1mo ago Changed 3421e35a9e79
2mo ago First seen · 996 lines · 93 tokens per session scan A ed8e78fa1acf

Subscribe to this mod's changes

implement-tool is a skill published in the GitHub repository evo-design/proto-tools (142 stars, last pushed 2d ago), licensed MIT. It adds 93 tokens to every session and 15,148 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientific bioengineering bioinformatics generative-biology machine-learning

implement-tool next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
implement-toolevo-design/proto-tools	Skill	142	2d ago	MIT	A	93	Claude Code
statistical-modelinginflexa-ai/inflexa	Skill	36	yesterday	Apache-2.0	A	26	Claude Code, Codex
cellxgene-census-queryPharMolix/OpenBioMed	Skill	1.1k	3mo ago	MIT	A	105	Claude Code, Codex
metabolomics-analysisLord1Egypt/scientific-agent-toolkit	Skill	3	5mo ago	MIT	A	65	Claude Code
neuroscience-imagingLord1Egypt/scientific-agent-toolkit	Skill	3	5mo ago	MIT	A	78	Claude Code
ngs-pipeline-managementLord1Egypt/scientific-agent-toolkit	Skill	3	5mo ago	MIT	A	72	Claude Code
omics-integrationLord1Egypt/scientific-agent-toolkit	Skill	3	5mo ago	MIT	A	74	Claude Code

proto-tools: Skill for Claude Code