converts SAM format to BAM format samtools sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} #if $source.index_source == "history": --ref_file=$source.ref_file #else --ref_file="None" #end if --output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} Locally cached History

**What it does** This tool uses the SAMTools_ toolkit to produce an indexed BAM file based on a sorted input SAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml