You are not Transporting Goods, Only you are selling. Railways doing transportation for you. you are just taking service. So be clear in your thoughts. you just move your goods in city, your godown to railway station only.
Transport of goods and passengers by rail will attract 5% tax under GST. Although it seems more than the current effective service tax of 4.5%, the effective GST liability will go down thanks to the mechanism of input tax credit which is now available on rail transport.
This will be exceptionally beneficial to the railways as there is no ITC available on transportation through Goods Transport Agencies (such as trucks). GST rate is also 5% on road transport thus making the rail freight more competitive.
Also it is important to note that your GST number should be on the invoice and they upload the same on GST portal.