I have simplified your code slightly and identified the problem. The option for the minimum number of leaves is set with "M", not "m". I discovered this by first querying the possible options
WOW(J48)
The pertinent output of which says:
-M <minimum number of instances>
Set minimum number of instances per leaf. (default 2)
The important part of your code then becomes:
J48( Target ~ Attr1 + Attr2 , data= input, control= Weka_control(M=1,U=TRUE))
J48 unpruned tree
------------------
Attr1 = 0302
| Attr2 = 1: target2 (1.0)
| Attr2 = 2: target1 (1.0)
Attr1 = 0320: target3 (1.0)
Number of Leaves : 3
Size of the tree : 5