Easiest way is to add a distinct tag for each input using the tags parameter and then use conditionals to ensure that the correct filters and outputs are applied. Something like this:
input {
jdbc {
...
tags =>["jdbc1"]
}
}
filter {
if "jdbc1" in [tags] {
...
}
}
output {
if "jdbc1" in [tags] {
elasticsearch {
...
}
}
}