The commander determines the event you will take with input from the health care professional. If your profile says swim-only he can send you back to see if the doc will let you do the bike (most likely the doc will allow it).
According to AR 350-1 paragraph 1-24e(4):
Soldiers with temporary profiles of long duration (more than 3 months) may also take an alternate test if approved by the commander and health care personnel. Soldiers must be given 3 months to prepare for the alternate test from either the date of the profile or the date recommended by health care person
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