Is it possible to create multiple index in single config file with different input locations?

Is it possible to create multiple index in single config file with different input locations?

yes
inputs have no bearing on you creating indexes

https://www.elastic.co/guide/en/logstash/current/plugins-outputs-elasticsearch.html#plugins-outputs-elasticsearch-index

just like it uses in the eample logstash-%{yyyy.mmm.dd} you can %{filedname}-%{yyyy.mm.ddd} or wrap each elastisearch output in an if statement like

if [type] =~ /mytype/{
elasticsearch {
....
.....
index=> "mytype-today"
}
}else{
elasticsearch {
....
.....
index=>"allothertypes-today"
}
}

of course I think it would be better to use field names to sort your data. you can add a field on your file input

input {
file {
path=/var/log/message
add_field => { "dst_index" , "myindex" }
}
file {
path=>/var/log/audit
add_field => {"dst_index", "someotherindex"}
}
}

output{
elasticsearch{
....
.....
index=>"%{dst_index}-%{yyyy.mm.ddd}"
}
}

I like this way cause it provides the most flexibility,