here is the modified query:
SELECT [Item] as Item#,
[ALF],[REJ_FG],[SFTO-618],[TOOL],[qty]
FROM(SELECT T0.[ItemCode] as Item, sum(T0.[TransValue]) AS Cost, T0.[Warehouse] AS WAREHOUSE,sum(T0.[InQty] - T0.[OutQty]) AS QTY
FROM OINM T0
WHERE T0.[DocDate] <= [%0] AND T0.[ItemCode] = [%1] group by T0.[ItemCode],T0.[Warehouse]) S
PIVOT
(SUM(cost) FOR WAREHOUSE IN ([ALF],[REJ_FG],[SFTO-618],[TOOL])) P