Output Engine

Output Engine

This skill manages all manuscript output formatting and export. It supports three output formats — Markdown, LaTeX, and DOCX — and handles venue-specific template selection, bibliography generation, figure integration, and supplementary material packaging.

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1. Markdown (Default Working Format)

Markdown is the default working format for all manuscript drafting. All section-writing skills produce Markdown output that is clean and paste-ready.

Format Conventions

• Headings: # for manuscript title, ## for major sections (Methods, Results, etc.), ### for subsections
• Bold: **text** for emphasis (used sparingly)
• Italic: *text* for journal names, statistical symbols, and gene/species names
• Tables: Pipe-delimited Markdown tables with header separator row
• Figures: Referenced by label: Figure 1, eFigure 1, not embedded as images
• Citations: Numbered in square brackets: [1], [2,3], [4-7]
• Supplementary: Clearly separated with a ## Supplementary Materials heading

Paste-Ready Output

When the user copies Markdown output into a manuscript:

• No raw HTML tags
• No code fences (except in supplementary code appendices)
• No emoji or special Unicode beyond standard scientific symbols (en-dash, multiplication sign, degree symbol)
• Clean line breaks: one blank line between paragraphs, no trailing whitespace

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2. LaTeX Export

2.1 Venue Template Selection

The LaTeX template is selected based on target_journal in PAPER_CONTEXT.md or user request. See references/latex-templates.md for detailed guidance.

Template	Target Journals	Document Class
Generic	Any journal not listed below	article with standard packages
JAMA	JAMA, JAMA Network Open, JAMA Internal Medicine	Custom JAMA class or article with JAMA formatting
Lancet	The Lancet, Lancet Infectious Diseases, Lancet Public Health	article with Lancet formatting

Template files are stored in templates/latex/. If no template exists for the requested journal, use the generic template and note: [NOTE: Using generic LaTeX template. Journal-specific formatting may need manual adjustment.]

2.2 Preamble Structure

Every LaTeX document includes:

\documentclass[12pt,a4paper]{article}

% Essential packages
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{times}              % Times New Roman font
\usepackage[margin=1in]{geometry}
\usepackage{setspace}           % Line spacing
\usepackage{graphicx}           % Figure inclusion
\usepackage{booktabs}           % Professional tables
\usepackage{amsmath}            % Mathematical notation
\usepackage{hyperref}           % DOI and URL links
\usepackage{natbib}             % Bibliography management
\usepackage{caption}            % Caption formatting
\usepackage{subcaption}         % Sub-figures

\doublespacing                  % Double-spaced by default

Additional packages are loaded as needed based on content (e.g., tikz for diagrams, longtable for multi-page tables, pdflscape for landscape pages).

2.3 BibTeX Generation

When exporting to LaTeX, generate a corresponding .bib file:

@article{page2021prisma,
  author    = {Page, Matthew J. and McKenzie, Joanne E. and Bossuyt, Patrick M.
               and Boutron, Isabelle and Hoffmann, Tammy C. and Mulrow, Cynthia D.
               and Shamseer, Larissa and Tetzlaff, Jennifer M. and Akl, Elie A.
               and Brennan, Sue E. and others},
  title     = {The {PRISMA} 2020 statement: an updated guideline for reporting
               systematic reviews},
  journal   = {BMJ},
  year      = {2021},
  volume    = {372},
  pages     = {n71},
  doi       = {10.1136/bmj.n71},
  pmid      = {33782057}
}

BibTeX key convention: firstauthorlastname + year + firstkeyword (all lowercase, no spaces).

2.4 Figure Integration

Figures are included using standard LaTeX float environments:

\begin{figure}[htbp]
  \centering
  \includegraphics[width=\textwidth]{figures/figure1.pdf}
  \caption{Caption text here.}
  \label{fig:figure1}
\end{figure}

• Prefer PDF or EPS vector formats for figures
• PNG/JPG acceptable at minimum 300 DPI
• Figures referenced via \ref{fig:figure1} in text

2.5 Supplementary Materials

Supplementary materials are placed in a separate section or file:

\clearpage
\section*{Supplementary Materials}
\setcounter{figure}{0}
\setcounter{table}{0}
\renewcommand{\thefigure}{e\arabic{figure}}
\renewcommand{\thetable}{e\arabic{table}}

This resets counters and prefixes with "e" for eFigure and eTable numbering.

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3. DOCX Export

3.1 Pandoc Detection

which pandoc

Run via Bash to detect whether pandoc is installed.

3.2 If Pandoc is Available

Convert Markdown to DOCX using a reference template:

pandoc manuscript.md \
  --reference-doc=templates/docx/reference.docx \
  --bibliography=references.bib \
  --csl=vancouver.csl \
  -o manuscript.docx

The reference.docx template defines:

• Font: Times New Roman, 12pt
• Spacing: Double-spaced throughout
• Margins: 1 inch (2.54 cm) on all sides
• Page numbers: Bottom centre, starting from title page
• Heading styles: Mapped from Markdown headings

See references/docx-templates.md for detailed template specifications.

3.3 If Pandoc is Not Available

Provide the user with instructions:

[DOCX EXPORT: Pandoc is not installed on this system. To convert to DOCX:

1. Install pandoc: https://pandoc.org/installing.html
2. Run: pandoc manuscript.md --reference-doc=templates/docx/reference.docx -o manuscript.docx

Alternatively, copy the Markdown output into Google Docs or Microsoft Word
and apply formatting manually.]

3.4 Deprecation Note

Per-command DOCX output (e.g., "write methods as DOCX") is deprecated. All DOCX conversion is handled via the /export-manuscript command, which processes the complete manuscript at once. This ensures consistent formatting across all sections.

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4. Export Workflow

When the user invokes /export-manuscript or "export manuscript":

Step 1 — Determine Output Format

1. Check output_format in PAPER_CONTEXT.md
2. If not specified, ask: "Which format? Markdown (default), LaTeX, or DOCX?"

Step 2 — Assemble Manuscript

1. Collect all drafted sections in expert writing order (Methods, Results, Discussion, Abstract, Introduction, Title, Captions, References)
2. Verify all sections are present; warn about missing sections
3. Run cross-reference check: figure/table mentions match actual figures/tables

Step 3 — Format and Export

Markdown:

• Combine sections into a single clean Markdown file
• Append reference list at the end
• Add supplementary materials after main text

LaTeX:

• Select venue template (Section 2.1)
• Generate preamble (Section 2.2)
• Convert each section to LaTeX
• Generate .bib file (Section 2.3)
• Integrate figures (Section 2.4)
• Add supplementary materials (Section 2.5)
• Output: .tex file + .bib file + figure files

DOCX:

• Detect pandoc (Section 3.1)
• Convert via pandoc with reference template (Section 3.2)
• Or provide manual instructions (Section 3.3)

Step 4 — Post-Export Checks

• Verify word counts for abstract and main text against journal limits
• Confirm all figures are referenced and files exist
• Confirm reference numbering is sequential and complete
• Report export location and any warnings

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5. Error Handling

Error Condition	Action
Missing sections in manuscript	Warn user with list of missing sections; export available sections with placeholders
Unknown target journal	Use generic template; note that manual formatting may be needed
Pandoc not installed	Provide installation instructions and manual conversion guidance
LaTeX compilation fails	Report error; suggest checking package dependencies
Figure files not found	Flag with [FIGURE MISSING: expected at <path>]
Word count exceeds journal limit	Report excess and suggest sections to trim

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References

• references/abstract-formats.md — Structured abstract formats for all supported journals
• references/latex-templates.md — LaTeX template selection and preamble guide
• references/docx-templates.md — DOCX template specifications and pandoc commands