Arguments : bam1, bam2
The two input files represent two mates of the same sample and they're prepared by the first step of hictool.
The path names should assume /data/. The output files will go to the /data/ directory as well, so mount the bam directory as /data/.
docker run -v /inputdir/:/data/:rw duplexa/hictool-bam2matrix /data/input.R1.bam /data/input.R2.bam