PBJelly_Batch_Protocol.xml

<jellyProtocol>
    <reference>/PATH/TO/ASSEMBLY/assembly.fasta</reference>  
    <outputDir>/PATH/TO/OUTPUT/DIR</outputDir>
    <blasr>-minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 8 -noSplitSubreads</blasr>
    <input baseDir="/PATH/TO/INPUT/DIR">
        <job>input.fastq</job>
    </input>
</jellyProtocol>