After a lot of digging around I finally ended up downloading the source code of the recovery section of Android. Turns out you can actually send commands to the recovery.
* The arguments which may be supplied in the recovery.command file:
* --send_intent=anystring - write the text out to recovery.intent
* --update_package=path - verify install an OTA package file
* --wipe_data - erase user data (and cache), then reboot
* --wipe_cache - wipe cache (but not user data), then reboot
* --set_encrypted_filesystem=on|off - enables / diasables encrypted fs
Those are the commands you can use according to the one I found but that might be different for modded files. So using adb you can do this:
adb shell
recovery --wipe_data
Using --wipe_data seemed to do what I was looking for which was handy although I have not fully tested this as of yet.
EDIT:
For anyone still using this topic, these commands may change based on which recovery you are using. If you are using Clockword recovery, these commands should still work. You can find other commands in /cache/recovery/command
For more information please see here:
https://github.com/CyanogenMod/android_bootable_recovery/blob/cm-10.2/recovery.c
