The example you are pointing to is discharging the battery from fully charged to fully discharged. By changing the sign of the pulse current the battery will be charging.
Check out the following example on MATLAB Central:
This example includes parameter estimation of single cell using pulsed discharge experiments.
Alternatively, you can check the Battery Parameter Extraction from Data example in Simscape Electrical where both charging and discharging pulses are used to extract battery parameters. I hope this helps.
