The cover letter is your first introduction to the publisher and should be as professional as possible. Make sure you keep it relevant; this is your chance to provide the publisher with your credentials as a writer.
It should state your real name, your pseudonym (if you’re writing under one), and any publishing credits you may have. If the story you’re submitting has been previously published (even if it was published by you), mention it in the cover letter. You will also want to introduce your submission—give the title, genre, word count, and a short blurb of the story.
In e-mail submissions, the cover letter should be the body of the e-mail. There’s no need to send it as a separate file unless the publisher requests it.
