Hello @Chath,
The flashing tool does offer a command line interface, you should be able to locate it in your S32DS installation directory, for example: C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\bin
you can run the following command for help:
S32FlashTool.exe -h
You can also open the command line tool using the GUI, this will give you some example command configurations once you have configured your target device:

For example:
# Retrieve existing COM ports
# S32FlashTool -i uart -p ?
# Retrieve connected, supported CAN adapters
# S32FlashTool -i can -p ?
# Retrieve Ethernet adapters
# S32FlashTool -i ethernet -p ?
# Load the target binary and read the MCUID
# S32FlashTool -t C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\targets\S32G3xxx.bin -i uart -p COM13 -mcuid
# Load the target binary and the flash memory algorithm
# S32FlashTool -t C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\targets\S32G3xxx.bin -a C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\flash\MX25UW51245G.bin -i uart -p COM13
# Read 0x100 bytes from the address 0x0000_0000 of the flash memory
# S32FlashTool -t C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\targets\S32G3xxx.bin -i uart -p COM13 -fread -addr 0x00000000 -size 0x100
# Upload (program) a file [FILE] to the flash memory starting with address 0x0000_0000
# S32FlashTool -t C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\targets\S32G3xxx.bin -i uart -p COM13 -fprogram -addr 0x00000000 -f [FILE]
# Upload a binary [FILE] to SRAM at address [ADDRESS] and execute it
# S32FlashTool -t C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\targets\S32G3xxx.bin -i uart -p COM13 -addr [ADDRESS] -boot [FILE]
C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\bin>
Please also check the available documentation in: C:\NXP\S32DS.3.5\S32DS\tools\S32FlashTool\doc
Regarding the S32DS compilation process, getting it to work can be somewhat difficult, I can recommend you check section Build configuration of the S32DS user guide [starting at page 231, C:/NXP/S32DS.3.5/S32DS/help/pdf/S32DS_User_Guide.pdf], in which you will be able to see all the configurations related to compiler, linker, assembler and all other compilation tools.
Let me know if you need more information about this topic.