[2] | 1 | <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.0.6"> |
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| 2 | <requirements><requirement type='package'>bowtie</requirement></requirements> |
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| 3 | <description></description> |
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| 4 | <command interpreter="python"> |
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| 5 | bowtie_wrapper.py |
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| 6 | --threads="4" |
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| 7 | --dataType="solexa" |
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| 8 | --output=$output |
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| 9 | --suppressHeader=$suppressHeader |
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| 10 | --genomeSource=$refGenomeSource.genomeSource |
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| 11 | --snpphred="None" |
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| 12 | --snpfrac="None" |
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| 13 | --keepends="None" |
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| 14 | #if $refGenomeSource.genomeSource == "history": |
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| 15 | #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): |
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| 16 | --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" |
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| 17 | --do_not_build_index |
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| 18 | #else: |
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| 19 | --ref=$refGenomeSource.ownFile |
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| 20 | --indexSettings=$refGenomeSource.indexParams.indexSettings |
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| 21 | #if $refGenomeSource.indexParams.indexSettings == "indexFull": |
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| 22 | --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB |
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| 23 | #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": |
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| 24 | --ipacked=$refGenomeSource.indexParams.autoBehavior.packed |
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| 25 | --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax |
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| 26 | --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn |
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| 27 | --idcv=$refGenomeSource.indexParams.autoBehavior.dcv |
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| 28 | #else: |
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| 29 | --ipacked="None" |
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| 30 | --ibmax="None" |
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| 31 | --ibmaxdivn="None" |
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| 32 | --idcv="None" |
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| 33 | #end if |
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| 34 | --inodc=$refGenomeSource.indexParams.nodc |
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| 35 | --inoref=$refGenomeSource.indexParams.noref |
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| 36 | --ioffrate=$refGenomeSource.indexParams.offrate |
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| 37 | --iftab=$refGenomeSource.indexParams.ftab |
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| 38 | --intoa=$refGenomeSource.indexParams.ntoa |
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| 39 | --iendian=$refGenomeSource.indexParams.endian |
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| 40 | --iseed=$refGenomeSource.indexParams.seed |
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| 41 | --icutoff=$refGenomeSource.indexParams.cutoff |
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| 42 | #else: |
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| 43 | --iautoB="None" |
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| 44 | --ipacked="None" |
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| 45 | --ibmax="None" |
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| 46 | --ibmaxdivn="None" |
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| 47 | --idcv="None" |
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| 48 | --inodc="None" |
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| 49 | --inoref="None" |
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| 50 | --ioffrate="None" |
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| 51 | --iftab="None" |
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| 52 | --intoa="None" |
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| 53 | --iendian="None" |
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| 54 | --iseed="None" |
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| 55 | --icutoff="None" |
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| 56 | #end if |
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| 57 | #end if |
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| 58 | #else: |
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| 59 | --ref=$refGenomeSource.index |
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| 60 | --indexSettings="None" |
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| 61 | --iautoB="None" |
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| 62 | --ipacked="None" |
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| 63 | --ibmax="None" |
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| 64 | --ibmaxdivn="None" |
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| 65 | --idcv="None" |
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| 66 | --inodc="None" |
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| 67 | --inoref="None" |
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| 68 | --ioffrate="None" |
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| 69 | --iftab="None" |
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| 70 | --intoa="None" |
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| 71 | --iendian="None" |
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| 72 | --iseed="None" |
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| 73 | --icutoff="None" |
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| 74 | #end if |
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| 75 | --paired=$singlePaired.sPaired |
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| 76 | #if $singlePaired.sPaired == "single": |
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| 77 | --input1=$singlePaired.sInput1 |
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| 78 | --input2="None" |
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| 79 | --params=$singlePaired.sParams.sSettingsType |
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| 80 | #if $singlePaired.sParams.sSettingsType == "full": |
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| 81 | --skip=$singlePaired.sParams.sSkip |
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| 82 | --alignLimit=$singlePaired.sParams.sAlignLimit |
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| 83 | --trimH=$singlePaired.sParams.sTrimH |
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| 84 | --trimL=$singlePaired.sParams.sTrimL |
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| 85 | --mismatchSeed=$singlePaired.sParams.sMismatchSeed |
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| 86 | --mismatchQual=$singlePaired.sParams.sMismatchQual |
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| 87 | --seedLen=$singlePaired.sParams.sSeedLen |
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| 88 | --rounding=$singlePaired.sParams.sRounding |
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| 89 | --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign |
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| 90 | --tryHard=$singlePaired.sParams.sTryHard |
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| 91 | --valAlign=$singlePaired.sParams.sValAlign |
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| 92 | --allValAligns=$singlePaired.sParams.sAllValAligns |
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| 93 | --suppressAlign=$singlePaired.sParams.sSuppressAlign |
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| 94 | --best=$singlePaired.sParams.sBestOption.sBest |
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| 95 | #if $singlePaired.sParams.sBestOption.sBest == "doBest": |
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| 96 | --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks |
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| 97 | --strata=$singlePaired.sParams.sBestOption.sdStrata |
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| 98 | #else: |
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| 99 | --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks |
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| 100 | --strata="None" |
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| 101 | #end if |
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| 102 | --offrate=$singlePaired.sParams.sOffrate |
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| 103 | --seed=$singlePaired.sParams.sSeed |
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| 104 | #else: |
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| 105 | --skip="None" |
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| 106 | --alignLimit="None" |
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| 107 | --trimH="None" |
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| 108 | --trimL="None" |
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| 109 | --mismatchSeed="None" |
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| 110 | --mismatchQual="None" |
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| 111 | --seedLen="None" |
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| 112 | --rounding="None" |
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| 113 | --maqSoapAlign="None" |
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| 114 | --tryHard="None" |
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| 115 | --valAlign="None" |
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| 116 | --allValAligns="None" |
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| 117 | --suppressAlign="None" |
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| 118 | --best="None" |
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| 119 | --maxBacktracks="None" |
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| 120 | --strata="None" |
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| 121 | --offrate="None" |
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| 122 | --seed="None" |
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| 123 | --snpphred="None" |
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| 124 | --snpfrac="None" |
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| 125 | --keepends="None" |
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| 126 | #end if |
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| 127 | --minInsert="None" |
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| 128 | --maxInsert="None" |
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| 129 | --mateOrient="None" |
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| 130 | --maxAlignAttempt="None" |
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| 131 | --forwardAlign="None" |
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| 132 | --reverseAlign="None" |
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| 133 | #else: |
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| 134 | --input1=$singlePaired.pInput1 |
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| 135 | --input2=$singlePaired.pInput2 |
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| 136 | --maxInsert=$singlePaired.pMaxInsert |
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| 137 | --mateOrient=$singlePaired.pMateOrient |
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| 138 | --params=$singlePaired.pParams.pSettingsType |
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| 139 | #if $singlePaired.pParams.pSettingsType == "full": |
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| 140 | --skip=$singlePaired.pParams.pSkip |
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| 141 | --alignLimit=$singlePaired.pParams.pAlignLimit |
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| 142 | --trimH=$singlePaired.pParams.pTrimH |
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| 143 | --trimL=$singlePaired.pParams.pTrimL |
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| 144 | --mismatchSeed=$singlePaired.pParams.pMismatchSeed |
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| 145 | --mismatchQual=$singlePaired.pParams.pMismatchQual |
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| 146 | --seedLen=$singlePaired.pParams.pSeedLen |
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| 147 | --rounding=$singlePaired.pParams.pRounding |
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| 148 | --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign |
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| 149 | --minInsert=$singlePaired.pParams.pMinInsert |
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| 150 | --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt |
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| 151 | --forwardAlign=$singlePaired.pParams.pForwardAlign |
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| 152 | --reverseAlign=$singlePaired.pParams.pReverseAlign |
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| 153 | --tryHard=$singlePaired.pParams.pTryHard |
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| 154 | --valAlign=$singlePaired.pParams.pValAlign |
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| 155 | --allValAligns=$singlePaired.pParams.pAllValAligns |
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| 156 | --suppressAlign=$singlePaired.pParams.pSuppressAlign |
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| 157 | --best=$singlePaired.pParams.pBestOption.pBest |
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| 158 | #if $singlePaired.pParams.pBestOption.pBest == "doBest": |
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| 159 | --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks |
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| 160 | --strata=$singlePaired.pParams.pBestOption.pdStrata |
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| 161 | #else: |
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| 162 | --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks |
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| 163 | --strata="None" |
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| 164 | #end if |
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| 165 | --offrate=$singlePaired.pParams.pOffrate |
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| 166 | --seed=$singlePaired.pParams.pSeed |
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| 167 | #else: |
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| 168 | --skip="None" |
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| 169 | --alignLimit="None" |
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| 170 | --trimH="None" |
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| 171 | --trimL="None" |
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| 172 | --mismatchSeed="None" |
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| 173 | --mismatchQual="None" |
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| 174 | --seedLen="None" |
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| 175 | --rounding="None" |
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| 176 | --maqSoapAlign="None" |
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| 177 | --tryHard="None" |
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| 178 | --valAlign="None" |
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| 179 | --allValAligns="None" |
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| 180 | --suppressAlign="None" |
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| 181 | --best="None" |
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| 182 | --maxBacktracks="None" |
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| 183 | --strata="None" |
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| 184 | --offrate="None" |
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| 185 | --seed="None" |
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| 186 | --minInsert="None" |
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| 187 | --maxAlignAttempt="None" |
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| 188 | --forwardAlign="None" |
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| 189 | --reverseAlign="None" |
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| 190 | #end if |
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| 191 | #end if |
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| 192 | </command> |
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| 193 | <inputs> |
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| 194 | <conditional name="refGenomeSource"> |
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| 195 | <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
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| 196 | <option value="indexed">Use a built-in index</option> |
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| 197 | <option value="history">Use one from the history</option> |
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| 198 | </param> |
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| 199 | <when value="indexed"> |
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| 200 | <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> |
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| 201 | <options from_data_table="bowtie_indexes"/> |
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| 202 | <!-- |
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| 203 | <options from_file="bowtie_indices.loc"> |
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| 204 | <column name="value" index="1" /> |
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| 205 | <column name="name" index="0" /> |
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| 206 | </options> |
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| 207 | --> |
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| 208 | </param> |
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| 209 | </when> |
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| 210 | <when value="history"> |
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| 211 | <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> |
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| 212 | <conditional name="indexParams"> |
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| 213 | <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> |
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| 214 | <option value="indexPreSet">Default</option> |
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| 215 | <option value="indexFull">Set your own</option> |
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| 216 | </param> |
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| 217 | <when value="indexPreSet" /> |
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| 218 | <when value="indexFull"> |
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| 219 | <conditional name="autoBehavior"> |
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| 220 | <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> |
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| 221 | <option value="auto">Automatic behavior</option> |
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| 222 | <option value="set">Set values (sets --noauto and allows others to be set)</option> |
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| 223 | </param> |
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| 224 | <when value="auto" /> |
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| 225 | <when value="set"> |
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| 226 | <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> |
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| 227 | <option value="unpacked">Use regular representation</option> |
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| 228 | <option value="packed">Use packed representation</option> |
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| 229 | </param> |
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| 230 | <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> |
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| 231 | <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> |
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| 232 | <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> |
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| 233 | </when> |
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| 234 | </conditional> |
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| 235 | <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> |
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| 236 | <option value="dc">Use difference-cover sample</option> |
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| 237 | <option value="nodc">Disable difference-cover sample</option> |
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| 238 | </param> |
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| 239 | <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> |
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| 240 | <option value="ref">Build all index files</option> |
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| 241 | <option value="noref">Do not build paired-end alignment index files</option> |
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| 242 | </param> |
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| 243 | <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> |
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| 244 | <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> |
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| 245 | <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> |
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| 246 | <option value="no">Do not convert Ns</option> |
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| 247 | <option value="yes">Convert Ns to As</option> |
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| 248 | </param> |
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| 249 | <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> |
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| 250 | <option value="little">Little</option> |
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| 251 | <option value="big">Big</option> |
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| 252 | </param> |
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| 253 | <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> |
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| 254 | <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> |
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| 255 | </when> <!-- indexFull --> |
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| 256 | </conditional> <!-- indexParams --> |
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| 257 | </when> <!-- history --> |
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| 258 | </conditional> <!-- refGenomeSource --> |
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| 259 | <conditional name="singlePaired"> |
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| 260 | <param name="sPaired" type="select" label="Is this library mate-paired?"> |
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| 261 | <option value="single">Single-end</option> |
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| 262 | <option value="paired">Paired-end</option> |
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| 263 | </param> |
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| 264 | <when value="single"> |
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| 265 | <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> |
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| 266 | <conditional name="sParams"> |
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| 267 | <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> |
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| 268 | <option value="preSet">Commonly used</option> |
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| 269 | <option value="full">Full parameter list</option> |
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| 270 | </param> |
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| 271 | <when value="preSet" /> |
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| 272 | <when value="full"> |
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| 273 | <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> |
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| 274 | <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> |
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| 275 | <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> |
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| 276 | <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> |
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| 277 | <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> |
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| 278 | <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> |
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| 279 | <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> |
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| 280 | <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> |
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| 281 | <option value="round">Round to nearest 10</option> |
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| 282 | <option value="noRound">Do not round to nearest 10</option> |
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| 283 | </param> |
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| 284 | <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> |
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| 285 | <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> |
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| 286 | <option value="noTryHard">Do not try hard</option> |
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| 287 | <option value="doTryHard">Try hard</option> |
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| 288 | </param> |
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| 289 | <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> |
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| 290 | <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> |
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| 291 | <option value="noAllValAligns">Do not report all valid alignments</option> |
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| 292 | <option value="doAllValAligns">Report all valid alignments</option> |
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| 293 | </param> |
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| 294 | <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> |
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| 295 | <conditional name="sBestOption"> |
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| 296 | <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
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| 297 | <option value="noBest">Do not use best</option> |
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| 298 | <option value="doBest">Use best</option> |
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| 299 | </param> |
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| 300 | <when value="noBest"> |
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| 301 | <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> |
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| 302 | </when> |
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| 303 | <when value="doBest"> |
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| 304 | <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> |
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| 305 | <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> |
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| 306 | <option value="noStrata">Do not use strata option</option> |
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| 307 | <option value="doStrata">Use strata option</option> |
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| 308 | </param> |
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| 309 | </when> |
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| 310 | </conditional> <!-- bestOption --> |
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| 311 | <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> |
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| 312 | <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
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| 313 | </when> <!-- full --> |
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| 314 | </conditional> <!-- sParams --> |
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| 315 | </when> <!-- single --> |
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| 316 | <when value="paired"> |
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| 317 | <param name="pInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> |
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| 318 | <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> |
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| 319 | <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> |
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| 320 | <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> |
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| 321 | <option value="fr">FR (for Illumina)</option> |
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| 322 | <option value="rf">RF</option> |
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| 323 | <option value="ff">FF (for SOLiD)</option> |
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| 324 | </param> |
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| 325 | <conditional name="pParams"> |
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| 326 | <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> |
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| 327 | <option value="preSet">Commonly used</option> |
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| 328 | <option value="full">Full parameter list</option> |
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| 329 | </param> |
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| 330 | <when value="preSet" /> |
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| 331 | <when value="full"> |
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| 332 | <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> |
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| 333 | <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> |
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| 334 | <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> |
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| 335 | <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> |
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| 336 | <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> |
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| 337 | <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> |
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| 338 | <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> |
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| 339 | <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> |
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| 340 | <option value="round">Round to nearest 10</option> |
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| 341 | <option value="noRound">Do not round to nearest 10</option> |
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| 342 | </param> |
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| 343 | <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> |
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| 344 | <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> |
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| 345 | <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> |
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| 346 | <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> |
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| 347 | <option value="forward">Align against the forward reference strand</option> |
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| 348 | <option value="noForward">Do not align against the forward reference strand</option> |
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| 349 | </param> |
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| 350 | <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> |
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| 351 | <option value="reverse">Align against the reverse-complement reference strand</option> |
---|
| 352 | <option value="noReverse">Do not align against the reverse-complement reference strand</option> |
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| 353 | </param> |
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| 354 | <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> |
---|
| 355 | <option value="noTryHard">Do not try hard</option> |
---|
| 356 | <option value="doTryHard">Try hard</option> |
---|
| 357 | </param> |
---|
| 358 | <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> |
---|
| 359 | <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> |
---|
| 360 | <option value="noAllValAligns">Do not report all valid alignments</option> |
---|
| 361 | <option value="doAllValAligns">Report all valid alignments</option> |
---|
| 362 | </param> |
---|
| 363 | <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> |
---|
| 364 | <conditional name="pBestOption"> |
---|
| 365 | <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
---|
| 366 | <option value="noBest">Do not use best</option> |
---|
| 367 | <option value="doBest">Use best</option> |
---|
| 368 | </param> |
---|
| 369 | <when value="noBest"> |
---|
| 370 | <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> |
---|
| 371 | </when> |
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| 372 | <when value="doBest"> |
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| 373 | <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> |
---|
| 374 | <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> |
---|
| 375 | <option value="noStrata">Do not use strata option</option> |
---|
| 376 | <option value="doStrata">Use strata option</option> |
---|
| 377 | </param> |
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| 378 | </when> |
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| 379 | </conditional> |
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| 380 | <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> |
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| 381 | <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
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| 382 | </when> <!-- full --> |
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| 383 | </conditional> <!-- pParams --> |
---|
| 384 | </when> <!-- paired --> |
---|
| 385 | </conditional> <!-- singlePaired --> |
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| 386 | <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> |
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| 387 | </inputs> |
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| 388 | <outputs> |
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| 389 | <data format="sam" name="output" > |
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| 390 | <actions> |
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| 391 | <conditional name="refGenomeSource.genomeSource"> |
---|
| 392 | <when value="indexed"> |
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| 393 | <action type="metadata" name="dbkey"> |
---|
| 394 | <option type="from_file" name="bowtie_indices.loc" column="0" offset="0"> |
---|
| 395 | <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
---|
| 396 | <filter type="param_value" ref="refGenomeSource.index" column="1"/> |
---|
| 397 | </option> |
---|
| 398 | </action> |
---|
| 399 | </when> |
---|
| 400 | </conditional> |
---|
| 401 | <!-- Special casing equCab2chrM to equCab2 --> |
---|
| 402 | <action type="metadata" name="dbkey"> |
---|
| 403 | <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0"> |
---|
| 404 | <filter type="insert_column" column="0" value="equCab2chrM"/> |
---|
| 405 | <filter type="insert_column" column="0" value="equCab2"/> |
---|
| 406 | <filter type="metadata_value" ref="output" name="dbkey" column="1" /> |
---|
| 407 | </option> |
---|
| 408 | </action> |
---|
| 409 | </actions> |
---|
| 410 | </data> |
---|
| 411 | </outputs> |
---|
| 412 | <tests> |
---|
| 413 | <test> |
---|
| 414 | <!-- |
---|
| 415 | Bowtie command: |
---|
| 416 | bowtie -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out2.sam |
---|
| 417 | -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. |
---|
| 418 | chrM_base needs to be the base location/name of the index files. |
---|
| 419 | --> |
---|
| 420 | <param name="genomeSource" value="indexed" /> |
---|
| 421 | <param name="index" value="equCab2chrM" /> |
---|
| 422 | <param name="sPaired" value="single" /> |
---|
| 423 | <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> |
---|
| 424 | <param name="sSettingsType" value="preSet" /> |
---|
| 425 | <param name="suppressHeader" value="true" /> |
---|
| 426 | <output name="output" ftype="sam" file="bowtie_out2.sam" /> |
---|
| 427 | </test> |
---|
| 428 | <test> |
---|
| 429 | <!-- |
---|
| 430 | Bowtie command: |
---|
| 431 | bowtie-build -f test-data/chr_m.fasta chrM_base |
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| 432 | bowtie -X 1000 +fr -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 -k 1 +best -p 4 -S +sam-nohead -q chrM_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > test-data/bowtie_out4.sam |
---|
| 433 | -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. |
---|
| 434 | chrM_base is the index files' location/base name. |
---|
| 435 | --> |
---|
| 436 | <param name="genomeSource" value="history" /> |
---|
| 437 | <param name="ownFile" value="chr_m.fasta" /> |
---|
| 438 | <param name="indexSettings" value="indexPreSet" /> |
---|
| 439 | <param name="sPaired" value="paired" /> |
---|
| 440 | <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> |
---|
| 441 | <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> |
---|
| 442 | <param name="pMaxInsert" value="1000" /> |
---|
| 443 | <param name="pMateOrient" value="fr" /> |
---|
| 444 | <param name="pSettingsType" value="full" /> |
---|
| 445 | <param name="pSkip" value="0" /> |
---|
| 446 | <param name="pAlignLimit" value="-1" /> |
---|
| 447 | <param name="pTrimH" value="0" /> |
---|
| 448 | <param name="pTrimL" value="0" /> |
---|
| 449 | <param name="pMismatchSeed" value="2" /> |
---|
| 450 | <param name="pMismatchQual" value="70" /> |
---|
| 451 | <param name="pSeedLen" value="28" /> |
---|
| 452 | <param name="pRounding" value="round" /> |
---|
| 453 | <param name="pMaqSoapAlign" value="-1" /> |
---|
| 454 | <param name="pMinInsert" value="0" /> |
---|
| 455 | <param name="pMaxAlignAttempt" value="100" /> |
---|
| 456 | <param name="pForwardAlign" value="forward" /> |
---|
| 457 | <param name="pReverseAlign" value="reverse" /> |
---|
| 458 | <param name="pTryHard" value="noTryHard" /> |
---|
| 459 | <param name="pValAlign" value="1" /> |
---|
| 460 | <param name="pAllValAligns" value="noAllValAligns" /> |
---|
| 461 | <param name="pSuppressAlign" value="-1" /> |
---|
| 462 | <param name="pBest" value="doBest" /> |
---|
| 463 | <param name="pdMaxBacktracks" value="800" /> |
---|
| 464 | <param name="pdStrata" value="noStrata" /> |
---|
| 465 | <param name="pOffrate" value="-1" /> |
---|
| 466 | <param name="pSeed" value="-1" /> |
---|
| 467 | <param name="suppressHeader" value="true" /> |
---|
| 468 | <output name="output" ftype="sam" file="bowtie_out4.sam" /> |
---|
| 469 | </test> |
---|
| 470 | <test> |
---|
| 471 | <!-- |
---|
| 472 | Bowtie command: |
---|
| 473 | bowtie -n 2 -e 70 -l 28 -k 1 +maxbts 125 -y -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out6.sam |
---|
| 474 | -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. |
---|
| 475 | chrM_base is the index files' location/base name. |
---|
| 476 | --> |
---|
| 477 | <param name="genomeSource" value="indexed" /> |
---|
| 478 | <param name="index" value="equCab2chrM" /> |
---|
| 479 | <param name="sPaired" value="single" /> |
---|
| 480 | <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> |
---|
| 481 | <param name="sSettingsType" value="full" /> |
---|
| 482 | <param name="sSkip" value="0" /> |
---|
| 483 | <param name="sAlignLimit" value="-1" /> |
---|
| 484 | <param name="sTrimH" value="0" /> |
---|
| 485 | <param name="sTrimL" value="0" /> |
---|
| 486 | <param name="sMismatchSeed" value="2" /> |
---|
| 487 | <param name="sMismatchQual" value="70" /> |
---|
| 488 | <param name="sSeedLen" value="28" /> |
---|
| 489 | <param name="sRounding" value="round" /> |
---|
| 490 | <param name="sMaqSoapAlign" value="-1" /> |
---|
| 491 | <param name="sTryHard" value="doTryHard" /> |
---|
| 492 | <param name="sValAlign" value="1" /> |
---|
| 493 | <param name="sAllValAligns" value="noAllValAligns" /> |
---|
| 494 | <param name="sSuppressAlign" value="-1" /> |
---|
| 495 | <param name="sBest" value="noBest" /> |
---|
| 496 | <param name="snMaxBacktracks" value="125" /> |
---|
| 497 | <param name="sOffrate" value="-1" /> |
---|
| 498 | <param name="sSeed" value="-1" /> |
---|
| 499 | <param name="suppressHeader" value="true" /> |
---|
| 500 | <output name="output" ftype="sam" file="bowtie_out6.sam" /> |
---|
| 501 | </test> |
---|
| 502 | <test> |
---|
| 503 | <!-- |
---|
| 504 | Bowtie command: |
---|
| 505 | bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/chr_m.fasta chrM_base |
---|
| 506 | bowtie -X 1000 +fr -p 4 -S +sam-nohead -q chrM_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > test-data/bowtie_out8.sam |
---|
| 507 | -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. |
---|
| 508 | chrM_base is the index files' location/base name. |
---|
| 509 | --> |
---|
| 510 | <param name="genomeSource" value="history" /> |
---|
| 511 | <param name="ownFile" value="chr_m.fasta" /> |
---|
| 512 | <param name="indexSettings" value="indexFull" /> |
---|
| 513 | <param name="autoB" value="auto" /> |
---|
| 514 | <param name="nodc" value="dc" /> |
---|
| 515 | <param name="noref" value="ref" /> |
---|
| 516 | <param name="offrate" value="5" /> |
---|
| 517 | <param name="ftab" value="10" /> |
---|
| 518 | <param name="ntoa" value="no" /> |
---|
| 519 | <param name="endian" value="little" /> |
---|
| 520 | <param name="seed" value="-1" /> |
---|
| 521 | <param name="cutoff" value="-1" /> |
---|
| 522 | <param name="sPaired" value="paired" /> |
---|
| 523 | <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> |
---|
| 524 | <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> |
---|
| 525 | <param name="pMaxInsert" value="1000" /> |
---|
| 526 | <param name="pMateOrient" value="fr" /> |
---|
| 527 | <param name="pSettingsType" value="preSet" /> |
---|
| 528 | <param name="suppressHeader" value="true" /> |
---|
| 529 | <output name="output" ftype="sam" file="bowtie_out8.sam" /> |
---|
| 530 | </test> |
---|
| 531 | </tests> |
---|
| 532 | |
---|
| 533 | <help> |
---|
| 534 | |
---|
| 535 | **What it does** |
---|
| 536 | |
---|
| 537 | Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. |
---|
| 538 | |
---|
| 539 | .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml |
---|
| 540 | |
---|
| 541 | ------ |
---|
| 542 | |
---|
| 543 | **Know what you are doing** |
---|
| 544 | |
---|
| 545 | .. class:: warningmark |
---|
| 546 | |
---|
| 547 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. |
---|
| 548 | |
---|
| 549 | .. __: http://bowtie-bio.sourceforge.net/index.shtml |
---|
| 550 | |
---|
| 551 | ------ |
---|
| 552 | |
---|
| 553 | **Input formats** |
---|
| 554 | |
---|
| 555 | Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. |
---|
| 556 | |
---|
| 557 | ------ |
---|
| 558 | |
---|
| 559 | **Outputs** |
---|
| 560 | |
---|
| 561 | The output is in SAM format, and has the following columns:: |
---|
| 562 | |
---|
| 563 | Column Description |
---|
| 564 | -------- -------------------------------------------------------- |
---|
| 565 | 1 QNAME Query (pair) NAME |
---|
| 566 | 2 FLAG bitwise FLAG |
---|
| 567 | 3 RNAME Reference sequence NAME |
---|
| 568 | 4 POS 1-based leftmost POSition/coordinate of clipped sequence |
---|
| 569 | 5 MAPQ MAPping Quality (Phred-scaled) |
---|
| 570 | 6 CIGAR extended CIGAR string |
---|
| 571 | 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) |
---|
| 572 | 8 MPOS 1-based Mate POSition |
---|
| 573 | 9 ISIZE Inferred insert SIZE |
---|
| 574 | 10 SEQ query SEQuence on the same strand as the reference |
---|
| 575 | 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) |
---|
| 576 | 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE |
---|
| 577 | |
---|
| 578 | The flags are as follows:: |
---|
| 579 | |
---|
| 580 | Flag Description |
---|
| 581 | ------ ------------------------------------- |
---|
| 582 | 0x0001 the read is paired in sequencing |
---|
| 583 | 0x0002 the read is mapped in a proper pair |
---|
| 584 | 0x0004 the query sequence itself is unmapped |
---|
| 585 | 0x0008 the mate is unmapped |
---|
| 586 | 0x0010 strand of the query (1 for reverse) |
---|
| 587 | 0x0020 strand of the mate |
---|
| 588 | 0x0040 the read is the first read in a pair |
---|
| 589 | 0x0080 the read is the second read in a pair |
---|
| 590 | 0x0100 the alignment is not primary |
---|
| 591 | |
---|
| 592 | It looks like this (scroll sideways to see the entire example):: |
---|
| 593 | |
---|
| 594 | QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT |
---|
| 595 | HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh |
---|
| 596 | HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh |
---|
| 597 | |
---|
| 598 | ------- |
---|
| 599 | |
---|
| 600 | **Bowtie settings** |
---|
| 601 | |
---|
| 602 | All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here. |
---|
| 603 | |
---|
| 604 | ------ |
---|
| 605 | |
---|
| 606 | **Bowtie parameter list** |
---|
| 607 | |
---|
| 608 | This is an exhaustive list of Bowtie options: |
---|
| 609 | |
---|
| 610 | For indexing (bowtie-build):: |
---|
| 611 | |
---|
| 612 | -a No auto behavior. Disable the default behavior where bowtie automatically |
---|
| 613 | selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according |
---|
| 614 | to the memory available. [off] |
---|
| 615 | --packed Packing. Use a packed representation for DNA strings. [auto] |
---|
| 616 | --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto] |
---|
| 617 | --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block |
---|
| 618 | expressed as a fraction of the length of the reference. [4] |
---|
| 619 | --dcv INT Difference-cover sample. Use INT as the period for the difference-cover |
---|
| 620 | sample. [1024] |
---|
| 621 | --nodc INT No difference-cover sample. Disable the difference-cover sample. [off] |
---|
| 622 | -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions |
---|
| 623 | of the index. Used only for paired-end alignment. [off] |
---|
| 624 | -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The |
---|
| 625 | indexer will mark every 2^INT rows. The marked rows correspond to rows on |
---|
| 626 | the genome. [5] |
---|
| 627 | -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range |
---|
| 628 | with respect to the first INT characters of the query. Ftab is 4^INT+1 |
---|
| 629 | bytes. [10] |
---|
| 630 | --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are |
---|
| 631 | simply excluded from the index and Bowtie will not find alignments that |
---|
| 632 | overlap them. [off] |
---|
| 633 | --big Endianness. Endianness to use when serializing integers to the index file. [off] |
---|
| 634 | --little Endianness. [--little] |
---|
| 635 | --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] |
---|
| 636 | --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative |
---|
| 637 | across sequences) and ignore the rest. [off] |
---|
| 638 | |
---|
| 639 | For aligning (bowtie):: |
---|
| 640 | |
---|
| 641 | -s INT Skip. Do not align the first INT reads or pairs in the input. [off] |
---|
| 642 | -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit] |
---|
| 643 | -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each |
---|
| 644 | read before alignment. [0] |
---|
| 645 | -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each |
---|
| 646 | read before alignment. [0] |
---|
| 647 | -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined |
---|
| 648 | with seed length option). Can be 0, 1, 2, or 3. [2] |
---|
| 649 | -e INT Mismatch quality. Maximum permitted total of quality values at mismatched |
---|
| 650 | read positions. Bowtie rounds quality values to the nearest 10 and saturates |
---|
| 651 | at 30. [70] |
---|
| 652 | -l INT Seed length. The number of bases on the high-quality end of the read to |
---|
| 653 | which the -n ceiling applies. Must be at least 5. [28] |
---|
| 654 | --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and |
---|
| 655 | saturate at 30. This options turns off that rounding. [off] |
---|
| 656 | -v INT MAQ- or SOAP-like alignment policy. This option turns off the default |
---|
| 657 | MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments |
---|
| 658 | with at most INT mismatches. [off] |
---|
| 659 | -I INT Minimum insert. The minimum insert size for valid paired-end alignments. |
---|
| 660 | Does checking on untrimmed reads if -5 or -3 is used. [0] |
---|
| 661 | -X INT Maximum insert. The maximum insert size for valid paired-end alignments. |
---|
| 662 | Does checking on untrimmed reads if -5 or -3 is used. [250] |
---|
| 663 | --fr Mate orientation. The upstream/downstream mate orientations for a valid |
---|
| 664 | paired-end alignment against the forward reference strand. [--fr] |
---|
| 665 | --rf Mate orientation. [off] |
---|
| 666 | --ff Mate orientation. [off] |
---|
| 667 | --pairtries INT Maximum alignment attempts for paired-end data. [100] |
---|
| 668 | --nofw No forward aligning. Choosing this option means that Bowtie will not attempt |
---|
| 669 | to align against the forward reference strand. [off] |
---|
| 670 | --norc No reverse-complement aligning. Setting this will mean that Bowtie will not |
---|
| 671 | attempt to align against the reverse-complement reference strand. [off] |
---|
| 672 | --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning |
---|
| 673 | a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best] |
---|
| 674 | -y Try hard. Try as hard as possible to find valid alignments when they exist, |
---|
| 675 | including paired-end alignments. [off] |
---|
| 676 | --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to |
---|
| 677 | store path descriptors in --best mode. [32] |
---|
| 678 | -k INT Valid alignments. The number of valid alignments per read or pair. [off] |
---|
| 679 | -a All valid alignments. Choosing this means that all valid alignments per read |
---|
| 680 | or pair will be reported. [off] |
---|
| 681 | -m INT Suppress alignments. Suppress all alignments for a particular read or pair |
---|
| 682 | if more than INT reportable alignments exist for it. [no limit] |
---|
| 683 | --best Best mode. Make Bowtie guarantee that reported singleton alignments are |
---|
| 684 | "best" in terms of stratum (the number of mismatches) and quality values at |
---|
| 685 | mismatched position. [off] |
---|
| 686 | --strata Best strata. When running in best mode, report alignments that fall into the |
---|
| 687 | best stratum if there are ones falling into more than one. [off] |
---|
| 688 | -o INT Offrate override. Override the offrate of the index with INT. Some row |
---|
| 689 | markings are discarded when index read into memory. INT must be greater than |
---|
| 690 | the value used to build the index (default: 5). [off] |
---|
| 691 | --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] |
---|
| 692 | --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of |
---|
| 693 | SNPs per base in the subject genome. [see --snpfrac] |
---|
| 694 | --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace |
---|
| 695 | alignments. [0.001] |
---|
| 696 | --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace |
---|
| 697 | alignments. [off] |
---|
| 698 | |
---|
| 699 | </help> |
---|
| 700 | </tool> |
---|