The cover letter is not just a formality, rather it is a chance for you to lobby for your manuscript so you must ensure that your involvement in writing that is no less than what you do for writing the content of your manuscript. The objective of your cover letter is quite important, it is a medium to impress or convince the editor to forward your write up for the review process. The personification of your cover letter is similar to it being the presenter of your manuscript to argue that it is good enough for the standards of the journal so it should highlight your most important findings. The cover letter is the first and most important medium to assure the editor that your document does not have any conflicting interests and should generate interest in your document in a way that the editor feels that it should be strongly considered for publication.
Here are some formal suggestions for the cover letter:
Have a formal address for the editor: you must address the editor formally and if possible try to get the name of the editor so you could address him my name formally. You can get that information from the net in most of the cases
Include important details of the manuscript in the first paragraph itself: you must ensure that the first paragraph should include the title of the manuscript, main authors and if possible the theme of the manuscript in brief. What kind of manuscript it is, is also important to add here and by the end of the second paragraph, you should briefly explain the rationale of your document in a very impressive and convincing way.
Justify why your document fits the journal: the next paragraph should bring out those facts about your manuscript which are not just its strength s but also make the journal a good choice to publish it and vice versa. You can highlight the clinical implications of your manuscript if the journal so demands it. It may be possible that your work may not be the perfect fit for the journal but you can still try to align the aim and scope of the journal with the underlying objective of the journal.
Closing paragraph: the closing paragraph should necessarily include the following things: the commitment of originality of your document, commitment of no publication of same manuscript elsewhere and no conflicting interests and in case the journal wants your recommendation of potential reviewers.