documentclass{article}
usepackage{amssymb,amsmath}
usepackage{ifxetex,ifluatex}
ifxetex
  usepackage{fontspec,xltxtra,xunicode}
  defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
else
  ifluatex
    usepackage{fontspec}
    defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  else
    usepackage[utf8]{inputenc}
  fi
fi
ifxetex
  usepackage[setpagesize=false, % page size defined by xetex
              unicode=false, % unicode breaks when used with xetex
              xetex]{hyperref}
else
  usepackage[unicode=true]{hyperref}
fi
hypersetup{breaklinks=true, pdfborder={0 0 0}}
setlength{parindent}{0pt}
setlength{parskip}{6pt plus 2pt minus 1pt}
setlength{emergencystretch}{3em}  % prevent overfull lines
setcounter{secnumdepth}{0}

[... my preamble ...]

pandoc -o output.tex input.txt --include-before-body=header.tex --include-after-body=footer.tex

pandoc -o output.tex --template=FILE input.txt

pandoc -D latex

pandoc -o output.tex --standalone input.txt

pandoc -o output.tex input.txt