Navigate to your ~/Library/TeXShop/Engines folder and duplicate the file pdflatexmk.engine to, say, pdflatexmk-shell.engine. Then open this file with TeXShop itself and add the -pdflatex="pdflatex --shell-escape %O %S" option: here's how the file should be:
#!/bin/bash
export TSBIN="$HOME/Library/TeXShop/bin/tslatexmk"
export LTMKBIN="$HOME/Library/TeXShop/bin/tslatexmk"
export LTMKEDIT="$HOME/Library/TeXShop/bin"
# make sure latexmkrcedit exists in bin
if [ ! -e "${LTMKEDIT}/latexmkrcedit" ] ; then
cp "${LTMKBIN}/latexmkrcDONTedit" "${LTMKEDIT}/latexmkrcedit"
fi
"${LTMKBIN}"/latexmk -pdf -r "${LTMKEDIT}/latexmkrcedit" -r "${TSBIN}/pdflatexmkrc" -pdflatex="pdflatex --shell-escape %O %S" "$1"
Now, if you start your document with
% !TEX TS-program = pdflatexmk-shell
the shell escape will be enabled.
Here's a copy of the console when a file with that magic line is processed:
Latexmk: This is Latexmk, John Collins, 2 July 2013, version: 4.37.
**** Report bugs etc to John Collins <collins at phys.psu.edu>. ****
Rule 'pdflatex': File changes, etc:
Non-existent destination files:
'bart.pdf'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex --shell-escape -recorder "bart.tex"'
------------
Latexmk: applying rule 'pdflatex'...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
\write18 enabled.
entering extended mode
(./bart.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/size10.clo)) (./bart.aux)
[1{/usr/local/texlive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(./bart.aux) )</usr/local/texlive/2013/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb>
Output written on bart.pdf (1 page, 11541 bytes).
Transcript written on bart.log.
Latexmk: Log file says output to 'bart.pdf'
Latexmk: All targets (bart.pdf) are up-to-date
The lines
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
\write18 enabled.
are the proof that shell escape is enabled.
Best Answer
There are multiple options:
latexmk -xelatex -latexoption="-shell-escape" documentlatexmk -xelatex -shell-escape document(this option is not listed in the normallatexmk -helpmenu, but you have to runlatexmk -showextraoptionsto see it)