Resolution:
Follow the below given steps to configure the SSL with File Adapter along with JMS transport mode.

1. Open the tibemsadmin.exe and create user “test” also set the password as “test” and make sure that the topic is created on which we are publishing and subscribing the messages. For example: test
2. We can create the user and grant permission with the following commands in tibemsadmin:
     >&gtcreate user test password=test
        >&gtGRANT TOPIC TOPIC_NAME user=test ALL

3. To configure the SSL configuration, import the following certificates located at    
     &ltems_home>\bin\certs into the SSL_certs folder already created in the FA project.

Select SSL_Cert folder then Go to Tools menu--> Trusted Certificates --> Import into  PEM Format.
                 a. client.cert.pem
                 b. client_root.cert.pem
                 c. server.cert.pem
                 d. server_root.cert.pem

4. Now create an identity for these certificates. To create the identity, go to project    
      root, under general palettes, drag the identity palette.
5.  While configuring the identity specify the following,
               a. Type – Identity File
              b. Url -- browse for &ltems_home>/bin/certs/ client_identity.p12  file
               c. File Type – PKCS12
              d. Password – password.
               e. Then apply

6. Go to JMS Session under the Advanced folder of the adapter instance. Check the  
      ‘Use SSL’ check box and browse for Configure SSL.
7.  Specify the following values to configure.
         a. Basic Tab
                   i. Trusted Certificates Folder – specify the SSL_certs folder
                                 ii. Identity – specify the identity file.
         b.  Advanced Tab
                   i. Uncheck the Verify Host Name option

8.  Apply the configuration.
9.  Start the EMS server from the command line using the below command and verify the EMS URLs.
     tibemsd –config tibemsdssl.conf

Please make sure that the authorization is enabled inside the tibemsdssl.conf file.

10. Now run the File Adapter instance from Designer Tester and verify the result.

Please find the attached sample project along with the input file jms_ssl.txt. The TIBCO products used for the tests are FA 5.6, TRA 5.5.4, EMS  4.4.0 and SDK 5.5.1