I'm not sure if I understood you right, but I guess you want something like this:

#!/bin/ksh
FILE=$1

COUNTER=1
perl ./program0 "${FILE}" "${FILE}.${COUNTER}"

while [ $COUNTER -lt "5" ] ; do
   perl ./program${COUNTER} ${FILE}.${COUNTER} ${FILE}.$(expr ${COUNTE
+R} + 1)
   COUNTER=$(expr $COUNTER + 1)
done
[download]

You could start it with script.sh<FILE> and it would call program1-5 and give you 5 output files, and the last one would have gone through all five...but shell-scripts are evil :)

giant