This is a docker image for emsar. (more info from https://github.com/parklab/emsar)
Mount the directory that contains input files with the -v option as you run it. Replace the host source directory name with the target directory name of the container when you refer to a file or a directory.
Your files transcriptome.rsh and sample.bam are in directory /home/duplexa/docker_emsar_test. The corresponding target directory in the container is /data.
docker run -v /home/duplexa/docker_emsar_test:/data:rw duplexa/emsar -P -B -I /data/transcriptome.rsh /data/out sample /data/sample.bam
The output files will be in /home/duplexa/docker_emsar_test/out.