how to call server control defined in web page through separate javascript file

You need to pass the ID of the control as a parameter of your javascript function.
 
For reference, see the code below.
 
Your Javascript file abc.js contains following
 

function abc(txtID) {
    alert(document.getElementById(txtID).value);
}

 
HTML page contains,
 

        <script src="abc.js" type="text/javascript"></script>
        <asp:textbox id="txtInput" runat="server" ></asp:textbox>
        <asp:button id="btn2" runat="server" text="Click Me" />

 
Then on your server side page load event
 

    protected void Page_Load(object sender, EventArgs e)
    {
        if (!IsPostBack)
        {
            btn2.Attributes.Add("onclick", "abc('" + txtInput.ClientID + "')");
        }
    }
 

 
That's it, You are done.
 

 
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