python '$__tool_directory__/bowtie_wrapper.py'
      ## Set number of threads
      --threads="\${GALAXY_SLOTS:-4}"
      ## Outputs
      --output="${output}"
      #if str( $singlePaired.sPaired ) == "single"
        #if $output_unmapped_reads_l
          --output_unmapped_reads="${output_unmapped_reads_l}"
        #end if
        #if $output_suppressed_reads_l
          --output_suppressed_reads="${output_suppressed_reads_l}"
        #end if
        --galaxy_input_format="${singlePaired.sInput1.ext}"
      #else
        #if $output_unmapped_reads_l and $output_unmapped_reads_r
          --output_unmapped_reads_l="${output_unmapped_reads_l}"
          --output_unmapped_reads_r="${output_unmapped_reads_r}"
        #end if
        #if $output_suppressed_reads_l and $output_suppressed_reads_l
          --output_suppressed_reads_l="${output_suppressed_reads_l}"
          --output_suppressed_reads_r="${output_suppressed_reads_r}"
        #end if
        --galaxy_input_format="${singlePaired.pInput1.ext}"
      #end if
      ## Inputs
      --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
      --suppressHeader="${suppressHeader}"
      --genomeSource="${refGenomeSource.genomeSource}"
      #if $refGenomeSource.genomeSource == "history":
        ##index already exists
        #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
          ##user previously built
          --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
          --do_not_build_index
        #else:
          ##build index on the fly
          --ref="${refGenomeSource.ownFile}"
          --indexSettings="${refGenomeSource.indexParams.indexSettings}"
          #if $refGenomeSource.indexParams.indexSettings == "indexFull":
            --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
            #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
              --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
              --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
              --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
              --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
            #end if
            --inodc="${refGenomeSource.indexParams.nodc}"
            --inoref="${refGenomeSource.indexParams.noref}"
            --ioffrate="${refGenomeSource.indexParams.offrate}"
            --iftab="${refGenomeSource.indexParams.ftab}"
            --intoa="${refGenomeSource.indexParams.ntoa}"
            --iendian="${refGenomeSource.indexParams.endian}"
            --iseed="${refGenomeSource.indexParams.seed}"
          #end if
        #end if
      #else
        ##use pre-built index
        --ref="${refGenomeSource.index.fields.path}"
      #end if
      --paired="${singlePaired.sPaired}"
      #if $singlePaired.sPaired == "single":
        --input1="${singlePaired.sInput1}"
        --params="${singlePaired.sParams.sSettingsType}"
        #if $singlePaired.sParams.sSettingsType == "full":
          --skip="${singlePaired.sParams.sSkip}"
          --alignLimit="${singlePaired.sParams.sAlignLimit}"
          --trimH="${singlePaired.sParams.sTrimH}"
          --trimL="${singlePaired.sParams.sTrimL}"
          #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
            --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
            --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
            --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
            --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
          #else
            --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
          #end if
          --forwardAlign="${singlePaired.sParams.sForwardAlign}"
          --reverseAlign="${singlePaired.sParams.sReverseAlign}"
          --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
          --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
          #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
            --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
          #end if
          --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
          --best="${singlePaired.sParams.sBestOption.sBest}"
          #if $singlePaired.sParams.sBestOption.sBest == "doBest":
            --strata="${singlePaired.sParams.sBestOption.sdStrata}"
            #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
              --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
            #end if
          #else:
            #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
              --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
            #end if
          #end if
          --offrate="${singlePaired.sParams.sOffrate}"
          --seed="${singlePaired.sParams.sSeed}"
        #end if
      #else:
        --input1="${singlePaired.pInput1}"
        --input2="${singlePaired.pInput2}"
        --maxInsert="${singlePaired.pMaxInsert}"
        --mateOrient="${singlePaired.pMateOrient}"
        --params="${singlePaired.pParams.pSettingsType}"
        #if $singlePaired.pParams.pSettingsType == "full":
          --skip="${singlePaired.pParams.pSkip}"
          --alignLimit="${singlePaired.pParams.pAlignLimit}"
          --trimH="${singlePaired.pParams.pTrimH}"
          --trimL="${singlePaired.pParams.pTrimL}"
          #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
            --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
            --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
            --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
            --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
          #else
            --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
          #end if
          --minInsert="${singlePaired.pParams.pMinInsert}"
          --forwardAlign="${singlePaired.pParams.pForwardAlign}"
          --reverseAlign="${singlePaired.pParams.pReverseAlign}"
          --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
          --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
          #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
            --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
          #end if
          --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
          --best="${singlePaired.pParams.pBestOption.pBest}"
          #if $singlePaired.pParams.pBestOption.pBest == "doBest":
            --strata="${singlePaired.pParams.pBestOption.pdStrata}"
            #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
              --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
              --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
            #end if
          #else:
            #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
              --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
              --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
            #end if
          #end if
          --offrate="${singlePaired.pParams.pOffrate}"
          --seed="${singlePaired.pParams.pSeed}"
        #end if
      #end if
      #if $save_mapping_stats
        --output_mapping_stats="$mapping_stats"
      #end if