The Tax Invoice will be of total value, however, GST will be payable on your service charge only, assuming the rest of the amount charged is a pure reimbursement of actual cost of Ticket charges. The taxable value may be determined in either of the following ways.

The Value of your service will have to be determined wither by Rule 6(3) or Rule 7 of Valuation rules:-

Rule 6(3) states as follows:-
The value of supply of services in relation to booking of tickets for travel by air provided by an air travel agent, shall be deemed to be an amount calculated at the rate of five percent. of the basic fare in the case of domestic bookings, and at the rate of ten per cent. of the basic fare in the case of international bookings of passage for travel by air. Explanation - For the purposes of this sub-rule, the expression “basic fare” means that part of the air fare on which commission is normally paid to the air travel agent by the airline.
OR
Rule 7:-
Value of supply of services in case of pure agent- Notwithstanding anything contained in these rules, the expenditure or costs incurred by a supplier as a pure agent of the recipient of supply shall be excluded from the value of supply, if conditions prescribed under rule 7 are complied with.