I mean that there is anomaly in pixel values of output band. For example, even if cloud and land pixels aren’t concerned by the band math expression (which is if invalid_algal2_tsm_ys then -9999 else algal_2) , their values changed after running the xml script. But all things work well when I execute the same band math expression in snap.
I attached a word file to illustrate my issue. You can see that cloud values were NaN and after apply the band math expression which has no relation with cloud, their values became float number (0.05…).