edtFTPj/PRO 1.5.0 includes a powerful scripting engine that allows users to list FTP commands in a text file, and then execute all the commands sequentially.
Here's a sample script that includes using the 'auth' command to switch to secure mode:
# Sample FTP script using FTP initially
# then changing to FTPS
#
set remotehost=edtmobile
set port=21
set user=javaftp
set password=javaftp
set connectmode=passive
set timeout=30
set protocol=ftp
set localdir=D:\work\tmp
# logging off = 0, highest level = 5
set loglevel=5
set logfile=D:\work\ftp-ssl\tmp\script.log
# connect to the server
# optional remotehost and port supplied
# override the params set earlier
open edtmobile 21
cd remote/test
# change to secure mode
auth tls
# force binary mode transfers
binary
# put the local file test.jar to the server as mytest.jar
put test.jar mytest.jar
# rename it
rename mytest.jar test2.jar
# and get it back as test3.jar in the local working directory
get test2.jar test3.jar
# delete all *.jar files in the current directory on
# the server
mdelete *.jar
# disconnect
close