is not diagnosed by a urine test but be urethral swab culture and examination of the swab. Other test useful in diagnosis is digital rectal exam (DRE) to inspect the prostate gland for swelling or infection. A urologist will be the best person to get it examined from.
The small bumps on the penis in the absence of any STD can be rash due to friction rub,folliculitis,cysts ,molluscum contagiosum(multiple, small, dome-shaped papules, often with a central depression or plug) or genital warts(caused by HPV infection).
Apply warm compresses,Neosporin ointment and calamine lotion and avoid messing with it.You can take anti-inflammatory pain killers like ibuprofen or acetaminophen. If the lumps persists then it will be best to get it evaluated from a dermatologist.
I hope it helps. Take care and God bless.