I don't know about any software which does exactly what you are trying to do; but MYOB accountant office will still require you to decide which way to treat your capital gains/losses. Keep in mind that you will need to have some sort of consistency when calculating gains/profits and losses.
I find importing eofy info from Etrade into excel gives me all the info I need. Putting B for buy and E for Sale in a column makes it easy to list by doing a sort. The if statement is also handy to list amount greater than 0 or lesser.
