Not citing code libraries used for paper
You have to clarify to yourself whether you "plug n'played" or did a real contribution. Hiding the contribution of others because it diminishes your own to a level where it's questionable were not only unethical in itself, it also would have the smell of plagiarism (because one would insinuate that one did all the work in the paper which is not cited by oneself). 

You are very correct to be concerned about that. If your work is sufficiently good/substantial to be published, it is sufficiently good/substantial even if all external tools used are mentioned. That being said, you could, in the paper, make clear what your contribution is and why it is nontrivial.