Yes, we can achieve this, as the EBS adapter is available in 12c (https://blogs.oracle.com/stevenchan/oracle-ebs-adapter-for-oracle-soa-suite-12c-now-available )
So the flow would be B2B -> SOA -> EBS.
to elaborate more
High level steps:
1. receive the message from FTP channel in B2B
2. translate the EDI Message into XML in B2B
3. post the message into JMS queue (available by default in B2B - B2B_IN_QUEUE)
4. In SOA, configure this JMS adapter to read from B2B_IN_QUEUE and EBS adapter to write into EBS.
Alternatively, if the EBS tables are accessiblt using DB adapter, you may want to use that, instead of EBS Adapter.
How to configure in B2B ?
1. Administration -> document : create a document definition, by uploading the ecs and xsd files
2. configure a listening channel for FTP in Administration -> listening channel
3. enable JMS queue with following flag Use JMS Queue as default = true (https://docs.oracle.com/cd/E15523_01/user.1111/e10229/bb_config.htm#XBBUG1422 )
4. create a partner in B2B
5. Associate the document definition with partner
6. create an agreement and deploy
There is no explicit step-by-step documentation, but this document (http://www.oracle.com/technetwork/middleware/b2b-integrations/learnmore/edicookbookoracle-b2b-11g-1662529.pdf ) will be of help.
Hope this helps
Thank You Dheeraj for your explanation.