In a js file you write javascript not html, so I'd say you'd do something like this:
myhtml.html
<html>
<head>
<title>sometitle</title>
<script type="text/javascript" src="myjsfile.js"></script>
</head>
<body>
<a href="javascript:MyFunction("google.co.uk",1)">method 1</a>
<a href="javascript:void(false)" onclick="MyFunction("google.co.uk",2)">method 2</a>
</body>
</html>
myjsfile.js
var win = null;
function MyFunction(url,method) {
alert("this is method "+method);
win = window.open(url,"popupwindow","scrollbars=1,status=1");
}
see
http://www.w3schools.com/jsref/met_win_open.asp for a detailed description of the window.open function

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