The old "engineer in a box" software request?
At first, your question seemed to deal with simply converting gas volume to mass units. However, it appears to be a fluid hydraulics analysis question.
As Haf indicated, it gets more complicated when friction losses come into play. Since you stated that the fluid flows through piping from one vessel (chamber?) to the other, frictional losses will likely be significant.
Hydraulic fluid analyses (pressure drops and flowrate calcs) are pretty standard for mechanical and chemical engineers. You may want to review fluid mechanics texts, or Perry's Handbook for Chemical Engineers, or perhaps Mark's handbook for Mechanical Engineers, or, Crane Technical Paper #410 (available for purchase from their web site). With an understanding of the problem (bournelli's equation, fanning friction factors, etc), software such as PIPENET from Sunrise Systems, or a host of others, can be purchased (Crane has a simple and inexpensive package), although you should likely just do it "by hand".
If you provided all the details, you may even find a fellow tipster here that may be set up to crunch the numbers for you, as a demonstration. You would need to describe the gas composition, inlet and outlet pressure and temperature, piping configuration (ID, material, length, valves, # bends, elevation change, etc), and one could then calculate the flowrate. If it is not steady state, iterations could be done as Haf suggested, using the appropriate methodology.
Is this a lab bench-scale operation or an industrial-scale steady-state operation? Need more detail.
Good luck.