wp_mail strips out the link url from the anchor tag in mail content

You are missing a single quote '

$activation_url="mobileappname://accesstoken#w34rdgtsrt5v6m;

should be…

$activation_url = "mobileappname://accesstoken#w34rdgtsrt5v6m';

or (using double quotes)…

$activation_url = "mobileappname://accesstoken#w34rdgtsrt5v6m";

Update:

See this codex entry for more: http://codex.wordpress.org/Function_Reference/wp_mail

add_filter( 'wp_mail_content_type', 'set_html_content_type' );
wp_mail( '[email protected]', 'The subject', '<p>The <em>HTML</em> message</p>' );
remove_filter( 'wp_mail_content_type', 'set_html_content_type' ); // reset content-type to to avoid conflicts -- http://core.trac.wordpress.org/ticket/23578

function set_html_content_type()
{
    return 'text/html';
}

Basically you need to remove the plain text filter and replace it with the text/html filter to properly parse the HTML content you are sending via e-mail.