What is fill-protocol?

A tool for filling existing Word forms used for research protocols, ethics applications, and grant proposals. It places content into the original document while preserving its tables, fonts, spacing, and page layout.

Populating .doc or .docx templates with protocol or application content, including converting older .doc files and keeping table rows from splitting across pages.

Rebuilding an institutional form can break its formatting and structure. Filling the supplied template keeps the document aligned with the institution's required design.

fill-protocol — Skill for Claude Code by Aperivue/medsci-skills

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add Aperivue/medsci-skills --skill fill-protocol

Clone the repo

git clone --depth 1 https://github.com/Aperivue/medsci-skills

Made for: Claude Code.

Or install medsci-submission, the plugin that ships this one along with the rest of its 6 skills.

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/aperivue/medsci-skills/fill-protocol/github.svg)](https://agentmods.dev/skills/aperivue/medsci-skills/fill-protocol)

Your own site

<a href="https://agentmods.dev/skills/aperivue/medsci-skills/fill-protocol"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/fill-protocol/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/aperivue/medsci-skills/fill-protocol"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/fill-protocol.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 57 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,753 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 3 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Privilege Escalation · line 56
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
medium Privilege Escalation · line 57
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
medium Privilege Escalation · line 58
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.

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	$0.00057	$0.01753
Opus 5.5	$0.00023	$0.00701
Sonnet 5.5	$0.00011	$0.00351
Haiku 4.5	$0.00006	$0.00175

Measured 21d ago against content hash dd6ff438de08, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

fill-protocol scanned grade A with 0 findings 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 21d ago.

The scan reads SKILL.md. This mod also ships 7 executable files (scripts/doc_to_docx.py, scripts/fill_form.py, scripts/inspect_template.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/fill-protocol/SKILL.md · 154 lines

How it starts

The opening of the file, as written. The whole thing — 154 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Fill-Protocol Skill

Core Principles (Do Not Violate)

Open the existing template — never create from scratch. Use Document(template_path), not Document(): rebuilding loses the header logo, custom margins, footer placeholders and page numbering. Replace cell/paragraph text in place; never a single cell.text = "value" assignment, which erases run-level styles (bold, color, eastAsia font).
Convert .doc → .docx via LibreOffice headless before any editing. pandoc -f doc is not supported; textutil corrupts table structure (merged cells dropped).
Match cells by left-label text, not row/column coordinates such as table.cell(2, 1). Templates evolve and coordinate matching breaks silently.
Apply cantSplit to every filled row so a row never breaks across pages.
For CJK languages, set the eastAsia font attribute, not just run.font.name, or Hangul/Kanji/Hanzi render in fallback fonts.
Validate every fill operation: resolve every [MISS] line and every WARN: line ([TABLE-MISS], [SECTION-MISS], [RAW-NEWLINE]) before the filled form is submitted.

Dependencies

Python packages docxtpl python-docx pyyaml are always required. LibreOffice is needed only for a legacy .doc template (~700 MB on macOS). The bundled setup.sh detects what is missing:

bash ${CLAUDE_SKILL_DIR}/setup.sh check     # report what's installed (read-only)
bash ${CLAUDE_SKILL_DIR}/setup.sh install   # install missing pieces (asks before each)

When invoking this skill on behalf of a user:

Skip LibreOffice entirely if the template is already .docx.
Before calling doc_to_docx.py, run setup.sh check. If LibreOffice is missing, ask the user before installing, because the cask is ~700 MB.
Never pass --yes to setup.sh install unless the user has explicitly authorized unattended installation in this session, because it installs without prompting.
If the user declines, ask them to convert the .doc manually (Word/LibreOffice/Pages → Save As → .docx) and re-run with the converted file.

Read the full file on GitHub · 154 lines

Files

What ships with it

10 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.

21d ago Changed dd6ff438de08
23d ago Changed · +15 lines 2d7082c97468
25d ago Changed · -108 lines · -35 tokens per session scan B → A 7df18088cb5f
1mo ago Changed · -2 lines 64880365203b
1mo ago First seen · 249 lines · 92 tokens per session scan B 848b3711a0d1

Subscribe to this mod's changes

fill-protocol is a skill published in the GitHub repository Aperivue/medsci-skills (349 stars, last pushed yesterday), licensed MIT. It adds 57 tokens to every session and 1,753 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Claude Code Documents biostatistics claude-skills clinical-research diagnostic-accuracy literature-review

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fill-protocol