A simple implementation with a perhaps more natural syntax:
\documentclass{article}
\usepackage{mathtools}
\DeclarePairedDelimiterX{\EllInner}[1]{(}{)}{%
\renewcommand{\with}{\,\delimsize|\,}%
#1%
}
\newcommand{\Ell}{F\EllInner}
\providecommand{\with}{}
\begin{document}
\[
\Ell{\varphi\with k^2} = \int_0^\varphi\frac{dt}{\sqrt{1-k^4\sin^2t}}
\qquad
\Ell*{\frac{\pi^2}{4}\with k^2}
\qquad
\Ell[\Big]{\frac{\pi^2}{4}\with k^2}
\]
\end{document}

If you prefer the two argument syntax, you can do with
\documentclass{article}
\usepackage{mathtools}
\DeclarePairedDelimiterX{\EllInner}[2]{(}{)}{%
#1\,\delimsize|\,#2%
}
\newcommand{\Ell}{F\EllInner}
\begin{document}
\[
\Ell{\varphi}{k^2} = \int_0^\varphi\frac{dt}{\sqrt{1-k^4\sin^2t}}
\qquad
\Ell*{\frac{\pi^2}{4}}{k^2}
\qquad
\Ell[\Big]{\frac{\pi^2}{4}}{k^2}
\]
\end{document}
You can also use | as the inner separator, with a slick trick. The caveat is that the expressions must not contain |, but they can contain \vert, \lvert or \rvert.
\documentclass{article}
\usepackage{mathtools}
\DeclarePairedDelimiterX{\EllInner}[1]{(}{)}{\activatebar #1}
\newcommand{\Ell}{F\EllInner}
\newcommand{\activatebar}{%
\begingroup\lccode`~=`| \lowercase{\endgroup\def~}{\,\delimsize\vert\,}%
\mathcode`|="8000
}
\begin{document}
\[
\Ell{\varphi | k^2} = \int_0^\varphi\frac{dt}{\sqrt{1-k^4\sin^2t}}
\qquad
\Ell*{\frac{\pi^2}{4} | k^2}
\qquad
\Ell[\Big]{\frac{\pi^2}{4} | k^2}
\]
\end{document}
mathtoolspackage, subsection 3.6. Edit: “fractals”? Or do you mean “fractions”? – GuM Nov 28 '16 at 22:15