RM_PATH=\$(which RepeatMasker) &&
    if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&

    if [ -z "\$RM_LIB_PATH" ] ; then RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries ; fi &&
    #if $repeat_source.source_type == "dfam_up":
      mkdir lib/ &&
      ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
      RM_LIB_PATH=\$(pwd)/lib &&
    #end if

    ln -s '${input_fasta}' rm_input.fasta &&

    RepeatMasker -dir \$(pwd)
    -libdir \$RM_LIB_PATH
    #if $repeat_source.source_type == "library":
      -lib '${repeat_source.repeat_lib}'
      -cutoff '${repeat_source.cutoff}'
    #else if $repeat_source.source_type == "dfam":
      #if $repeat_source.species_source.species_from_list == 'yes':
        -species $repeat_source.species_source.species_list
      #else
        -species '${repeat_source.species_source.species_name}'
      #end if
    #else if $repeat_source.source_type == "dfam_up":
        -species '${repeat_source.species_name}'
    #end if
    -parallel \${GALAXY_SLOTS:-1}
    ${gff}
    ${excln}
    ${advanced.is_only}
    ${advanced.is_clip}
    ${advanced.no_is}
    ${advanced.rodspec}
    ${advanced.primspec}
    ${advanced.nolow}
    ${advanced.noint}
    ${advanced.norna}
    ${advanced.alu}
    ${advanced.div}
    ${advanced.search_speed}
    -frag ${advanced.frag}
    ## -maxsize ${advanced.maxsize}
    #if str($advanced.gc):
      -gc ${advanced.gc}
    #end if
    ${advanced.gccalc}
    ${advanced.nocut}
    ${advanced.keep_alignments}
    ${advanced.invert_alignments}
    ${advanced.xout}
    ${xsmall}
    ${advanced.poly}
    rm_input.fasta &&
    #if $advanced.is_only != '-is_only':
      mv rm_input.fasta.masked '${output_masked_genome}' &&
      sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ;  1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in  query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
      mv rm_input.fasta.tbl '${output_table}' &&
      #if $gff == '-gff':
        mv rm_input.fasta.out.gff '${output_gff}' &&
      #end if
      #if $advanced.keep_alignments == '-ali':
        mv rm_input.fasta.align '${output_alignment}' &&
      #end if
      #if $advanced.poly == '-poly':
        sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
      #end if
    #end if
    if [ -f 'rm_input.fasta.cat.gz' ]; then
      zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
    else
      mv rm_input.fasta.cat '${output_repeat_catalog}';
    fi