If you want to get the output from the Explorer, you use "Command", if
you want to filter your data, you use "Filter command" and when you
want to train a classifier, you use "Meta-classifier command".
In your case, the command therefore would something like this (no output file!):
java -classpath weka.jar weka.attributeSelection.InfoGainAttributeEval
-s "weka.attributeSelection.Ranker -T -1.7976931348623157E308 -N -1"
That you received the same data in "output.arff" as you used as input
via "input.arff" is expected, as the "Ranker" only ranks the
attributes, but doesn't actually modify the data itself.
Rule of thumb: "SubsetEval" schemes will modify the dataset,
"AttributeEval" schemes can be used for ranking.