Paired-end data is processed with lumpyexpress using only the required arguments. Single-end data is processed with lumpy using -mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20. Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools
Split reads and discordant reads are extracted from the supplied bam files. Each bam file should represent a different sample.
This is a wrapper for lumpyexpress that comes with lumpy-sv version 0.2.13. The script in the latest version of lumpy-sv (0.2.14a) has some issues when run on galaxy.