annotate enhanced_bowtie_wrapper 1.0.0.xml @ 1:e28f8c08e736 draft

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author kaymccoy
date Sun, 07 Aug 2016 10:30:01 -0400
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1
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1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">
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2 <requirements>
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3 <requirement type="package" version="0.12.7">bowtie</requirement>
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4 </requirements>
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5 <description></description>
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6 <version_command>bowtie --version</version_command>
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7 <command interpreter="python">
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8 bowtie_wrapper.py
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9 ## Set number of threads
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10 --threads="\${GALAXY_SLOTS:-4}"
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11 ## Outputs
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12
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13
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14
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15
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16 #if "${singlePaired.sParams.outtype}" == "S"
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17 --output="${outputS}"
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18 #else
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19 --output="${outputM}"
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20 #end if
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21
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22
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23
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24 #if str( $singlePaired.sPaired ) == "single"
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25 #if $output_unmapped_reads_l
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26 --output_unmapped_reads="${output_unmapped_reads_l}"
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27 #end if
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28 #if $output_suppressed_reads_l
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29 --output_suppressed_reads="${output_suppressed_reads_l}"
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30 #end if
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31 --galaxy_input_format="${singlePaired.sInput1.ext}"
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32 #else
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33 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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34 --output_unmapped_reads_l="${output_unmapped_reads_l}"
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35 --output_unmapped_reads_r="${output_unmapped_reads_r}"
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36 #end if
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37 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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38 --output_suppressed_reads_l="${output_suppressed_reads_l}"
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39 --output_suppressed_reads_r="${output_suppressed_reads_r}"
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40 #end if
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41 --galaxy_input_format="${singlePaired.pInput1.ext}"
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42 #end if
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43 ## Inputs
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44 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
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45 --suppressHeader="${suppressHeader}"
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46 --genomeSource="${refGenomeSource.genomeSource}"
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47 #if $refGenomeSource.genomeSource == "history":
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48 ##index already exists
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49 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
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50 ##user previously built
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51 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
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52 --do_not_build_index
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53 #else:
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54 ##build index on the fly
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55 --ref="${refGenomeSource.ownFile}"
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56 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
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57 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
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58 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
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59 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
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60 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
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61 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
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62 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
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63 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
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64 #end if
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65 --inodc="${refGenomeSource.indexParams.nodc}"
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66 --inoref="${refGenomeSource.indexParams.noref}"
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67 --ioffrate="${refGenomeSource.indexParams.offrate}"
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68 --iftab="${refGenomeSource.indexParams.ftab}"
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69 --intoa="${refGenomeSource.indexParams.ntoa}"
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70 --iendian="${refGenomeSource.indexParams.endian}"
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71 --iseed="${refGenomeSource.indexParams.seed}"
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72 #end if
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73 #end if
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74 #else
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75 ##use pre-built index
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76 --ref="${refGenomeSource.index.fields.path}"
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77 #end if
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78 --paired="${singlePaired.sPaired}"
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79 #if $singlePaired.sPaired == "single":
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80
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81
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82
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83
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84
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85 --filetype="${singlePaired.sParams.filetype}"
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86 --outtype="${singlePaired.sParams.outtype}"
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87
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88
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89
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90 --input1="${singlePaired.sInput1}"
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91 --params="${singlePaired.sParams.sSettingsType}"
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92 #if $singlePaired.sParams.sSettingsType == "full":
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93 --skip="${singlePaired.sParams.sSkip}"
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94 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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95 --trimH="${singlePaired.sParams.sTrimH}"
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96 --trimL="${singlePaired.sParams.sTrimL}"
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97 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
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98 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
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99 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
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100 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
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101 --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
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102 #else
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103 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
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104 #end if
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105 --forwardAlign="${singlePaired.sParams.sForwardAlign}"
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106 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
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107 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
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108 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
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109 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
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110 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
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111 #end if
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112 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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113 --best="${singlePaired.sParams.sBestOption.sBest}"
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114 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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115 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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116 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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117 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
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118 #end if
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119 #else:
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120 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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121 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
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122 #end if
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123 #end if
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124 --offrate="${singlePaired.sParams.sOffrate}"
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125 --seed="${singlePaired.sParams.sSeed}"
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126 #end if
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127 #else:
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128 --input1="${singlePaired.pInput1}"
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129 --input2="${singlePaired.pInput2}"
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130 --maxInsert="${singlePaired.pMaxInsert}"
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131 --mateOrient="${singlePaired.pMateOrient}"
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132 --params="${singlePaired.pParams.pSettingsType}"
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133 #if $singlePaired.pParams.pSettingsType == "full":
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134 --skip="${singlePaired.pParams.pSkip}"
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135 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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136 --trimH="${singlePaired.pParams.pTrimH}"
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137 --trimL="${singlePaired.pParams.pTrimL}"
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138 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
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139 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
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140 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
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141 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
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142 --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
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143 #else
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144 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
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145 #end if
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146 --minInsert="${singlePaired.pParams.pMinInsert}"
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147 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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148 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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149 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
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150 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
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151 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
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152 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
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153 #end if
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154 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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155 --best="${singlePaired.pParams.pBestOption.pBest}"
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156 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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157 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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158 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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159 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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160 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
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161 #end if
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162 #else:
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163 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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164 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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165 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
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166 #end if
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167 #end if
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168 --offrate="${singlePaired.pParams.pOffrate}"
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169 --seed="${singlePaired.pParams.pSeed}"
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170 #end if
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171 #end if
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172 </command>
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173 <inputs>
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174 <conditional name="refGenomeSource">
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175 <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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176 <option value="indexed">Use a built-in index</option>
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177 <option value="history">Use one from the history</option>
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178 </param>
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179 <when value="indexed">
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180 <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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kaymccoy
parents:
diff changeset
181 <options from_data_table="bowtie_indexes">
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kaymccoy
parents:
diff changeset
182 <filter type="sort_by" column="2" />
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kaymccoy
parents:
diff changeset
183 <validator type="no_options" message="No indexes are available" />
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kaymccoy
parents:
diff changeset
184 </options>
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kaymccoy
parents:
diff changeset
185 </param>
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kaymccoy
parents:
diff changeset
186 </when>
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kaymccoy
parents:
diff changeset
187 <when value="history">
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kaymccoy
parents:
diff changeset
188 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
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kaymccoy
parents:
diff changeset
189 <conditional name="indexParams">
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kaymccoy
parents:
diff changeset
190 <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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kaymccoy
parents:
diff changeset
191 <option value="indexPreSet">Default</option>
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kaymccoy
parents:
diff changeset
192 <option value="indexFull">Set your own</option>
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kaymccoy
parents:
diff changeset
193 </param>
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kaymccoy
parents:
diff changeset
194 <when value="indexPreSet" />
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kaymccoy
parents:
diff changeset
195 <when value="indexFull">
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kaymccoy
parents:
diff changeset
196 <conditional name="autoBehavior">
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kaymccoy
parents:
diff changeset
197 <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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kaymccoy
parents:
diff changeset
198 <option value="auto">Automatic behavior</option>
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kaymccoy
parents:
diff changeset
199 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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kaymccoy
parents:
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200 </param>
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kaymccoy
parents:
diff changeset
201 <when value="auto" />
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kaymccoy
parents:
diff changeset
202 <when value="set">
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kaymccoy
parents:
diff changeset
203 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower">
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kaymccoy
parents:
diff changeset
204 <option value="unpacked">Use regular representation</option>
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kaymccoy
parents:
diff changeset
205 <option value="packed">Use packed representation</option>
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kaymccoy
parents:
diff changeset
206 </param>
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kaymccoy
parents:
diff changeset
207 <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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kaymccoy
parents:
diff changeset
208 <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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kaymccoy
parents:
diff changeset
209 <param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" />
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kaymccoy
parents:
diff changeset
210 </when>
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kaymccoy
parents:
diff changeset
211 </conditional>
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kaymccoy
parents:
diff changeset
212 <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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kaymccoy
parents:
diff changeset
213 <option value="dc">Use difference-cover sample</option>
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kaymccoy
parents:
diff changeset
214 <option value="nodc">Disable difference-cover sample</option>
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kaymccoy
parents:
diff changeset
215 </param>
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kaymccoy
parents:
diff changeset
216 <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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kaymccoy
parents:
diff changeset
217 <option value="ref">Build all index files</option>
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kaymccoy
parents:
diff changeset
218 <option value="noref">Do not build paired-end alignment index files</option>
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kaymccoy
parents:
diff changeset
219 </param>
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kaymccoy
parents:
diff changeset
220 <param name="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" />
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kaymccoy
parents:
diff changeset
221 <param name="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size is 4^(n+1) bytes" />
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kaymccoy
parents:
diff changeset
222 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
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kaymccoy
parents:
diff changeset
223 <option value="no">Do not convert Ns</option>
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kaymccoy
parents:
diff changeset
224 <option value="yes">Convert Ns to As</option>
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kaymccoy
parents:
diff changeset
225 </param>
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kaymccoy
parents:
diff changeset
226 <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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kaymccoy
parents:
diff changeset
227 <option value="little">Little</option>
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kaymccoy
parents:
diff changeset
228 <option value="big">Big</option>
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kaymccoy
parents:
diff changeset
229 </param>
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kaymccoy
parents:
diff changeset
230 <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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kaymccoy
parents:
diff changeset
231 </when> <!-- indexFull -->
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kaymccoy
parents:
diff changeset
232 </conditional> <!-- indexParams -->
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kaymccoy
parents:
diff changeset
233 </when> <!-- history -->
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kaymccoy
parents:
diff changeset
234 </conditional> <!-- refGenomeSource -->
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kaymccoy
parents:
diff changeset
235 <conditional name="singlePaired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
236 <param name="sPaired" type="select" label="Is this library mate-paired?">
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kaymccoy
parents:
diff changeset
237 <option value="single">Single-end</option>
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kaymccoy
parents:
diff changeset
238 <option value="paired">Paired-end</option>
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kaymccoy
parents:
diff changeset
239 </param>
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kaymccoy
parents:
diff changeset
240 <when value="single">
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kaymccoy
parents:
diff changeset
241 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fasta" label="FASTA or FASTQ file"/>
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kaymccoy
parents:
diff changeset
242 <conditional name="sParams">
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kaymccoy
parents:
diff changeset
243 <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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kaymccoy
parents:
diff changeset
244 <option value="preSet">Commonly used</option>
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kaymccoy
parents:
diff changeset
245 <option value="full">Full parameter list</option>
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kaymccoy
parents:
diff changeset
246 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
247 <when value="preSet" />
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kaymccoy
parents:
diff changeset
248 <when value="full">
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kaymccoy
parents:
diff changeset
249
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kaymccoy
parents:
diff changeset
250
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kaymccoy
parents:
diff changeset
251
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kaymccoy
parents:
diff changeset
252
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kaymccoy
parents:
diff changeset
253
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kaymccoy
parents:
diff changeset
254
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kaymccoy
parents:
diff changeset
255
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kaymccoy
parents:
diff changeset
256 <param name="filetype" type="select" label="Is your input file FASTA or FASTQ?">
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kaymccoy
parents:
diff changeset
257 <option value="f">FASTA</option>
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kaymccoy
parents:
diff changeset
258 <option value="q">FASTQ</option>
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kaymccoy
parents:
diff changeset
259 </param>
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kaymccoy
parents:
diff changeset
260 <param name="outtype" type="select" label="Should the output be in map or SAM format?">
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kaymccoy
parents:
diff changeset
261 <option value="">map</option>
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kaymccoy
parents:
diff changeset
262 <option value="S">SAM</option>
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kaymccoy
parents:
diff changeset
263 </param>
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kaymccoy
parents:
diff changeset
264
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kaymccoy
parents:
diff changeset
265
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kaymccoy
parents:
diff changeset
266
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kaymccoy
parents:
diff changeset
267
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kaymccoy
parents:
diff changeset
268
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kaymccoy
parents:
diff changeset
269 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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kaymccoy
parents:
diff changeset
270 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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kaymccoy
parents:
diff changeset
271 <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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kaymccoy
parents:
diff changeset
272 <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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kaymccoy
parents:
diff changeset
273 <conditional name="alignModeOption">
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kaymccoy
parents:
diff changeset
274 <param name="alignMode" type="select" label="Alignment mode">
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kaymccoy
parents:
diff changeset
275 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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kaymccoy
parents:
diff changeset
276 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
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kaymccoy
parents:
diff changeset
277 </param>
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kaymccoy
parents:
diff changeset
278 <when value="nMode">
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kaymccoy
parents:
diff changeset
279 <param name="sMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
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kaymccoy
parents:
diff changeset
280 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
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kaymccoy
parents:
diff changeset
281 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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kaymccoy
parents:
diff changeset
282 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
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kaymccoy
parents:
diff changeset
283 <option value="round">Round to nearest 10</option>
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kaymccoy
parents:
diff changeset
284 <option value="noRound">Do not round to nearest 10</option>
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kaymccoy
parents:
diff changeset
285 </param>
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kaymccoy
parents:
diff changeset
286 </when>
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kaymccoy
parents:
diff changeset
287 <when value="vMode">
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kaymccoy
parents:
diff changeset
288 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
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kaymccoy
parents:
diff changeset
289 </when>
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kaymccoy
parents:
diff changeset
290 </conditional>
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kaymccoy
parents:
diff changeset
291 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
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kaymccoy
parents:
diff changeset
292 <option value="forward">Align against the forward reference strand</option>
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kaymccoy
parents:
diff changeset
293 <option value="noForward">Do not align against the forward reference strand</option>
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kaymccoy
parents:
diff changeset
294 </param>
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kaymccoy
parents:
diff changeset
295 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
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kaymccoy
parents:
diff changeset
296 <option value="reverse">Align against the reverse-complement reference strand</option>
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kaymccoy
parents:
diff changeset
297 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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kaymccoy
parents:
diff changeset
298 </param>
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kaymccoy
parents:
diff changeset
299 <conditional name="sBestOption">
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kaymccoy
parents:
diff changeset
300 <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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kaymccoy
parents:
diff changeset
301 <option value="noBest">Do not use best</option>
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kaymccoy
parents:
diff changeset
302 <option value="doBest">Use best</option>
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kaymccoy
parents:
diff changeset
303 </param>
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kaymccoy
parents:
diff changeset
304 <when value="noBest">
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kaymccoy
parents:
diff changeset
305 <conditional name="sTryHardOption">
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kaymccoy
parents:
diff changeset
306 <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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kaymccoy
parents:
diff changeset
307 <option value="noTryHard">Do not try hard</option>
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kaymccoy
parents:
diff changeset
308 <option value="doTryHard">Try hard</option>
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kaymccoy
parents:
diff changeset
309 </param>
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kaymccoy
parents:
diff changeset
310 <when value="noTryHard">
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kaymccoy
parents:
diff changeset
311 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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kaymccoy
parents:
diff changeset
312 </when>
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kaymccoy
parents:
diff changeset
313 <when value="doTryHard" />
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kaymccoy
parents:
diff changeset
314 </conditional>
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kaymccoy
parents:
diff changeset
315 </when>
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kaymccoy
parents:
diff changeset
316 <when value="doBest">
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kaymccoy
parents:
diff changeset
317 <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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kaymccoy
parents:
diff changeset
318 <option value="noStrata">Do not use strata option</option>
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kaymccoy
parents:
diff changeset
319 <option value="doStrata">Use strata option</option>
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kaymccoy
parents:
diff changeset
320 </param>
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kaymccoy
parents:
diff changeset
321 <conditional name="sTryHardOption">
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kaymccoy
parents:
diff changeset
322 <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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kaymccoy
parents:
diff changeset
323 <option value="noTryHard">Do not try hard</option>
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kaymccoy
parents:
diff changeset
324 <option value="doTryHard">Try hard</option>
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kaymccoy
parents:
diff changeset
325 </param>
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kaymccoy
parents:
diff changeset
326 <when value="noTryHard">
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kaymccoy
parents:
diff changeset
327 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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kaymccoy
parents:
diff changeset
328 </when>
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kaymccoy
parents:
diff changeset
329 <when value="doTryHard" />
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kaymccoy
parents:
diff changeset
330 </conditional>
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kaymccoy
parents:
diff changeset
331 </when>
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kaymccoy
parents:
diff changeset
332 </conditional> <!-- bestOption -->
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kaymccoy
parents:
diff changeset
333 <conditional name="sAllValAlignsOption">
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kaymccoy
parents:
diff changeset
334 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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kaymccoy
parents:
diff changeset
335 <option value="noAllValAligns">Do not report all valid alignments</option>
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kaymccoy
parents:
diff changeset
336 <option value="doAllValAligns">Report all valid alignments</option>
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kaymccoy
parents:
diff changeset
337 </param>
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kaymccoy
parents:
diff changeset
338 <when value="noAllValAligns">
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kaymccoy
parents:
diff changeset
339 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
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kaymccoy
parents:
diff changeset
340 </when>
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kaymccoy
parents:
diff changeset
341 <when value="doAllValAligns" />
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kaymccoy
parents:
diff changeset
342 </conditional>
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kaymccoy
parents:
diff changeset
343 <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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kaymccoy
parents:
diff changeset
344 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
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kaymccoy
parents:
diff changeset
345 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
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kaymccoy
parents:
diff changeset
346 <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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kaymccoy
parents:
diff changeset
347 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
348 </when> <!-- full -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
349 </conditional> <!-- sParams -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
350 </when> <!-- single -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
351 <when value="paired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
352 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
353 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
354 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
355 <column name="name" index="0"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
356 <column name="value" index="0"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
357 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
358 </options>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
359 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
360 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
361 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
362 <option value="fr">FR (for Illumina)</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
363 <option value="rf">RF</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
364 <option value="ff">FF (for SOLiD)</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
365 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
366 <conditional name="pParams">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
367 <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">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
368 <option value="preSet">Commonly used</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
369 <option value="full">Full parameter list</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
370 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
371 <when value="preSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
372 <when value="full">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
373 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
374 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
375 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
376 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
377 <conditional name="alignModeOption">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
378 <param name="alignMode" type="select" label="Alignment mode">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
379 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
380 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
381 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
382 <when value="nMode">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
383 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
384 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
385 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
386 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
387 <option value="round">Round to nearest 10</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
388 <option value="noRound">Do not round to nearest 10</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
389 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
390 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
391 <when value="vMode">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
392 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
393 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
394 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
395 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
396 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
397 <option value="forward">Align against the forward reference strand</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
398 <option value="noForward">Do not align against the forward reference strand</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
399 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
400 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
401 <option value="reverse">Align against the reverse-complement reference strand</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
402 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
403 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
404 <conditional name="pBestOption">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
405 <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">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
406 <option value="noBest">Do not use best</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
407 <option value="doBest">Use best</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
408 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
409 <when value="noBest">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
410 <conditional name="pTryHardOption">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
411 <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">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
412 <option value="noTryHard">Do not try hard</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
413 <option value="doTryHard">Try hard</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
414 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
415 <when value="noTryHard">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
416 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
417 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
418 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
419 <when value="doTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
420 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
421 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
422 <when value="doBest">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
423 <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)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
424 <option value="noStrata">Do not use strata option</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
425 <option value="doStrata">Use strata option</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
426 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
427 <conditional name="pTryHardOption">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
428 <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">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
429 <option value="noTryHard">Do not try hard</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
430 <option value="doTryHard">Try hard</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
431 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
432 <when value="noTryHard">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
433 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
434 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
435 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
436 <when value="doTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
437 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
438 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
439 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
440 <conditional name="pAllValAlignsOption">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
441 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
442 <option value="noAllValAligns">Do not report all valid alignments</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
443 <option value="doAllValAligns">Report all valid alignments</option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
444 </param>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
445 <when value="noAllValAligns">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
446 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
447 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
448 <when value="doAllValAligns" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
449 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
450 <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" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
451 <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
452 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
453 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
454 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
455 </when> <!-- full -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
456 </conditional> <!-- pParams -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
457 </when> <!-- paired -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
458 </conditional> <!-- singlePaired -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
459 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
460 </inputs>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
461 <outputs>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
462
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
463
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
464
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
465
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
466
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
467
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
468 <data format="map" name="outputM" label="${tool.name} on ${on_string}: mapped reads"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
469 <data format="sam" name="outputS" label="${tool.name} on ${on_string}: mapped reads">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
470
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
471
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
472
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
473
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
474
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
475
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
476 <actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
477 <conditional name="refGenomeSource.genomeSource">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
478 <when value="indexed">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
479 <action type="metadata" name="dbkey">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
480 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
481 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
482 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
483 </option>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
484 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
485 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
486 <when value="history">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
487 <action type="metadata" name="dbkey">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
488 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
489 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
490 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
491 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
492 </actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
493 </data>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
494 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
495 <filter>((
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
496 singlePaired['sPaired'] == "single" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
497 singlePaired['sParams']['sSettingsType'] == "full" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
498 singlePaired['sParams']['sMaxFile'] is True
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
499 ) or (
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
500 singlePaired['sPaired'] == "paired" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
501 singlePaired['pParams']['pSettingsType'] == "full" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
502 singlePaired['pParams']['pMaxFile'] is True
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
503 ))
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
504 </filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
505 <actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
506 <conditional name="singlePaired.sPaired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
507 <when value="single">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
508 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
509 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
510 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
511 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
512 <when value="paired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
513 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
514 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
515 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
516 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
517 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
518 </actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
519 </data>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
520 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
521 <filter>singlePaired['sPaired'] == "paired"</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
522 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
523 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
524 <actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
525 <conditional name="singlePaired.sPaired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
526 <when value="single">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
527 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
528 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
529 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
530 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
531 <when value="paired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
532 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
533 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
534 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
535 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
536 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
537 </actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
538 </data>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
539 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
540 <filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
541 ((
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
542 singlePaired['sPaired'] == "single" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
543 singlePaired['sParams']['sSettingsType'] == "full" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
544 singlePaired['sParams']['sUnmappedFile'] is True
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
545 ) or (
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
546 singlePaired['sPaired'] == "paired" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
547 singlePaired['pParams']['pSettingsType'] == "full" and
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
548 singlePaired['pParams']['pUnmappedFile'] is True
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
549 ))
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
550 </filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
551 <actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
552 <conditional name="singlePaired.sPaired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
553 <when value="single">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
554 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
555 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
556 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
557 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
558 <when value="paired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
559 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
560 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
561 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
562 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
563 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
564 </actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
565 </data>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
566 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
567 <filter>singlePaired['sPaired'] == "paired"</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
568 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
569 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
570 <actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
571 <conditional name="singlePaired.sPaired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
572 <when value="single">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
573 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
574 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
575 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
576 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
577 <when value="paired">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
578 <action type="format">
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
579 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
580 </action>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
581 </when>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
582 </conditional>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
583 </actions>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
584 </data>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
585 </outputs>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
586 <tests>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
587 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
588 <!--
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
589 Bowtie command:
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
590 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
591 sort bowtie_out6_u.sam > bowtie_out6.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
592 -p is the number of threads. You need to replace the + with 2 dashes.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
593 chrM_base needs to be the base location/name of the index files.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
594 -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
595 <param name="genomeSource" value="indexed" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
596 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
597 <param name="index" value="equCab2chrM" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
598 <param name="sPaired" value="single" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
599 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
600 <param name="sSettingsType" value="preSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
601 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
602 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
603 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
604 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
605 <!--
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
606 Bowtie command:
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
607 bowtie-build -f test-data/phiX.fasta phiX_base
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
608 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
609 sort bowtie_out7_u.sam > bowtie_out7.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
610 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
611 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
612 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
613 -p is the number of threads. You need to replace the + with 2 dashes.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
614 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
615 chrM_base is the index files' location/base name.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
616 -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
617 <param name="genomeSource" value="history" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
618 <param name="ownFile" value="phiX.fasta" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
619 <param name="indexSettings" value="indexPreSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
620 <param name="sPaired" value="paired" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
621 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
622 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
623 <param name="pMaxInsert" value="1000" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
624 <param name="pMateOrient" value="ff" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
625 <param name="pSettingsType" value="full" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
626 <param name="pSkip" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
627 <param name="pAlignLimit" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
628 <param name="pTrimH" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
629 <param name="pTrimL" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
630 <param name="alignMode" value="nMode" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
631 <param name="pMismatchSeed" value="2" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
632 <param name="pMismatchQual" value="70" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
633 <param name="pSeedLen" value="28" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
634 <param name="pRounding" value="round" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
635 <param name="pMinInsert" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
636 <param name="pMaxAlignAttempt" value="100" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
637 <param name="pForwardAlign" value="forward" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
638 <param name="pReverseAlign" value="reverse" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
639 <param name="pTryHard" value="noTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
640 <param name="pValAlign" value="1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
641 <param name="pAllValAligns" value="noAllValAligns" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
642 <param name="pSuppressAlign" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
643 <param name="pUnmappedFile" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
644 <param name="pMaxFile" value="false" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
645 <param name="pBest" value="doBest" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
646 <param name="pdMaxBacktracks" value="800" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
647 <param name="pdStrata" value="noStrata" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
648 <param name="pOffrate" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
649 <param name="pSeed" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
650 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
651 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
652 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
653 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
654 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
655 <!-- start testing of non-sanger variant fastq reads -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
656 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
657 <param name="genomeSource" value="history" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
658 <param name="ownFile" value="phiX.fasta" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
659 <param name="indexSettings" value="indexPreSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
660 <param name="sPaired" value="paired" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
661 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
662 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
663 <param name="pMaxInsert" value="1000" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
664 <param name="pMateOrient" value="ff" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
665 <param name="pSettingsType" value="full" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
666 <param name="pSkip" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
667 <param name="pAlignLimit" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
668 <param name="pTrimH" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
669 <param name="pTrimL" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
670 <param name="alignMode" value="nMode" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
671 <param name="pMismatchSeed" value="2" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
672 <param name="pMismatchQual" value="70" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
673 <param name="pSeedLen" value="28" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
674 <param name="pRounding" value="round" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
675 <param name="pMinInsert" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
676 <param name="pMaxAlignAttempt" value="100" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
677 <param name="pForwardAlign" value="forward" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
678 <param name="pReverseAlign" value="reverse" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
679 <param name="pTryHard" value="noTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
680 <param name="pValAlign" value="1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
681 <param name="pAllValAligns" value="noAllValAligns" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
682 <param name="pSuppressAlign" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
683 <param name="pUnmappedFile" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
684 <param name="pMaxFile" value="false" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
685 <param name="pBest" value="doBest" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
686 <param name="pdMaxBacktracks" value="800" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
687 <param name="pdStrata" value="noStrata" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
688 <param name="pOffrate" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
689 <param name="pSeed" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
690 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
691 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
692 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
693 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
694 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
695 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
696 <param name="genomeSource" value="history" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
697 <param name="ownFile" value="phiX.fasta" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
698 <param name="indexSettings" value="indexPreSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
699 <param name="sPaired" value="paired" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
700 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
701 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
702 <param name="pMaxInsert" value="1000" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
703 <param name="pMateOrient" value="ff" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
704 <param name="pSettingsType" value="full" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
705 <param name="pSkip" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
706 <param name="pAlignLimit" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
707 <param name="pTrimH" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
708 <param name="pTrimL" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
709 <param name="alignMode" value="nMode" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
710 <param name="pMismatchSeed" value="2" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
711 <param name="pMismatchQual" value="70" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
712 <param name="pSeedLen" value="28" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
713 <param name="pRounding" value="round" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
714 <param name="pMinInsert" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
715 <param name="pMaxAlignAttempt" value="100" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
716 <param name="pForwardAlign" value="forward" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
717 <param name="pReverseAlign" value="reverse" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
718 <param name="pTryHard" value="noTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
719 <param name="pValAlign" value="1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
720 <param name="pAllValAligns" value="noAllValAligns" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
721 <param name="pSuppressAlign" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
722 <param name="pUnmappedFile" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
723 <param name="pMaxFile" value="false" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
724 <param name="pBest" value="doBest" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
725 <param name="pdMaxBacktracks" value="800" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
726 <param name="pdStrata" value="noStrata" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
727 <param name="pOffrate" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
728 <param name="pSeed" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
729 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
730 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
731 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
732 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
733 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
734 <!-- end testing of non-sanger variant fastq reads -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
735 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
736 <!--
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
737 Bowtie command:
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
738 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
739 sort bowtie_out9_u.sam > bowtie_out9.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
740 -p is the number of threads. You need to replace the + with 2 dashes.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
741 chrM_base is the index files' location/base name.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
742 -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
743 <param name="genomeSource" value="indexed" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
744 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
745 <param name="index" value="equCab2chrM" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
746 <param name="sPaired" value="single" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
747 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
748 <param name="sSettingsType" value="full" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
749 <param name="sSkip" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
750 <param name="sAlignLimit" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
751 <param name="sTrimH" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
752 <param name="sTrimL" value="0" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
753 <param name="alignMode" value="nMode" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
754 <param name="sMismatchSeed" value="2" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
755 <param name="sMismatchQual" value="70" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
756 <param name="sSeedLen" value="28" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
757 <param name="sRounding" value="round" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
758 <param name="sForwardAlign" value="forward" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
759 <param name="sReverseAlign" value="reverse" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
760 <param name="sTryHard" value="doTryHard" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
761 <param name="sValAlign" value="1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
762 <param name="sAllValAligns" value="noAllValAligns" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
763 <param name="sSuppressAlign" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
764 <param name="sUnmappedFile" value="false" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
765 <param name="sMaxFile" value="false" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
766 <param name="sBest" value="noBest" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
767 <param name="sOffrate" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
768 <param name="sSeed" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
769 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
770 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
771 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
772 <test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
773 <!--
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
774 Bowtie command:
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
775 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
776 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
777 sort bowtie_out10_u.sam > bowtie_out10.sam
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
778 -p is the number of threads. You need to replace the + with 2 dashes.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
779 chrM_base is the index files' location/base name.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
780 -->
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
781 <param name="genomeSource" value="history" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
782 <param name="ownFile" value="phiX.fasta" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
783 <param name="indexSettings" value="indexFull" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
784 <param name="autoB" value="auto" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
785 <param name="nodc" value="dc" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
786 <param name="noref" value="ref" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
787 <param name="offrate" value="5" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
788 <param name="ftab" value="10" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
789 <param name="ntoa" value="no" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
790 <param name="endian" value="little" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
791 <param name="seed" value="-1" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
792 <param name="sPaired" value="paired" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
793 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
794 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
795 <param name="pMaxInsert" value="1000" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
796 <param name="pMateOrient" value="ff" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
797 <param name="pSettingsType" value="preSet" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
798 <param name="suppressHeader" value="true" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
799 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
800 </test>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
801 </tests>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
802
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
803 <help>
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
804
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
805 **What it does**
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
806
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
807 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.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
808
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
809 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
810
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
811 ------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
812
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
813 **Know what you are doing**
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
814
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
815 .. class:: warningmark
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
816
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
817 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.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
818
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
819 .. __: http://bowtie-bio.sourceforge.net/index.shtml
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
820
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
821 ------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
822
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
823 **Input formats**
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
824
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
825 Bowtie accepts files in Sanger FASTQ or FASTA format.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
826
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
827 ------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
828
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
829 **A Note on Built-in Reference Genomes**
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
830
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
831 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
832
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
833 ------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
834
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
835 **Outputs**
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
836
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
837 The output is in SAM format, and has the following columns::
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
838
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
839 Column Description
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
840 -------- --------------------------------------------------------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
841 1 QNAME Query (pair) NAME
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
842 2 FLAG bitwise FLAG
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
843 3 RNAME Reference sequence NAME
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
844 4 POS 1-based leftmost POSition/coordinate of clipped sequence
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
845 5 MAPQ MAPping Quality (Phred-scaled)
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
846 6 CIGAR extended CIGAR string
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
847 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
848 8 MPOS 1-based Mate POSition
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
849 9 ISIZE Inferred insert SIZE
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
850 10 SEQ query SEQuence on the same strand as the reference
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
851 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
852 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
853
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
854 The flags are as follows::
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
855
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
856 Flag Description
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
857 ------ -------------------------------------
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
858 0x0001 the read is paired in sequencing
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
859 0x0002 the read is mapped in a proper pair
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
860 0x0004 the query sequence itself is unmapped
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
861 0x0008 the mate is unmapped
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
862 0x0010 strand of the query (1 for reverse)
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kaymccoy
parents:
diff changeset
863 0x0020 strand of the mate
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
864 0x0040 the read is the first read in a pair
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
865 0x0080 the read is the second read in a pair
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kaymccoy
parents:
diff changeset
866 0x0100 the alignment is not primary
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
867
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
868 It looks like this (scroll sideways to see the entire example)::
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kaymccoy
parents:
diff changeset
869
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
870 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
871 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
872 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
873
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kaymccoy
parents:
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874 -------
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kaymccoy
parents:
diff changeset
875
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kaymccoy
parents:
diff changeset
876 **Bowtie settings**
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kaymccoy
parents:
diff changeset
877
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kaymccoy
parents:
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878 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
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kaymccoy
parents:
diff changeset
879
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kaymccoy
parents:
diff changeset
880 ------
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kaymccoy
parents:
diff changeset
881
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kaymccoy
parents:
diff changeset
882 **Bowtie parameter list**
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kaymccoy
parents:
diff changeset
883
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kaymccoy
parents:
diff changeset
884 This is an exhaustive list of Bowtie options:
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kaymccoy
parents:
diff changeset
885
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kaymccoy
parents:
diff changeset
886 For indexing (bowtie-build)::
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kaymccoy
parents:
diff changeset
887
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kaymccoy
parents:
diff changeset
888 -a No auto behavior. Disable the default behavior where bowtie automatically
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kaymccoy
parents:
diff changeset
889 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
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kaymccoy
parents:
diff changeset
890 to the memory available. [off]
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kaymccoy
parents:
diff changeset
891 --packed Packing. Use a packed representation for DNA strings. [auto]
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kaymccoy
parents:
diff changeset
892 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
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kaymccoy
parents:
diff changeset
893 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
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kaymccoy
parents:
diff changeset
894 expressed as a fraction of the length of the reference. [4]
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kaymccoy
parents:
diff changeset
895 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
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kaymccoy
parents:
diff changeset
896 sample. [1024]
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kaymccoy
parents:
diff changeset
897 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
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kaymccoy
parents:
diff changeset
898 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
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kaymccoy
parents:
diff changeset
899 of the index. Used only for paired-end alignment. [off]
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kaymccoy
parents:
diff changeset
900 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
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kaymccoy
parents:
diff changeset
901 indexer will mark every 2^INT rows. The marked rows correspond to rows on
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kaymccoy
parents:
diff changeset
902 the genome. [5]
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kaymccoy
parents:
diff changeset
903 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
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kaymccoy
parents:
diff changeset
904 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
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kaymccoy
parents:
diff changeset
905 bytes. [10]
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kaymccoy
parents:
diff changeset
906 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
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kaymccoy
parents:
diff changeset
907 simply excluded from the index and Bowtie will not find alignments that
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kaymccoy
parents:
diff changeset
908 overlap them. [off]
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kaymccoy
parents:
diff changeset
909 --big Endianness. Endianness to use when serializing integers to the index file. [off]
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kaymccoy
parents:
diff changeset
910 --little Endianness. [--little]
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kaymccoy
parents:
diff changeset
911 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
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kaymccoy
parents:
diff changeset
912
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
913 For aligning (bowtie)::
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kaymccoy
parents:
diff changeset
914
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kaymccoy
parents:
diff changeset
915 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
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kaymccoy
parents:
diff changeset
916 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
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kaymccoy
parents:
diff changeset
917 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
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kaymccoy
parents:
diff changeset
918 read before alignment. [0]
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kaymccoy
parents:
diff changeset
919 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
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kaymccoy
parents:
diff changeset
920 read before alignment. [0]
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kaymccoy
parents:
diff changeset
921 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
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kaymccoy
parents:
diff changeset
922 with seed length option). Can be 0, 1, 2, or 3. [2]
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kaymccoy
parents:
diff changeset
923 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
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kaymccoy
parents:
diff changeset
924 read positions. Bowtie rounds quality values to the nearest 10 and saturates
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kaymccoy
parents:
diff changeset
925 at 30. [70]
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kaymccoy
parents:
diff changeset
926 -l INT Seed length. The number of bases on the high-quality end of the read to
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kaymccoy
parents:
diff changeset
927 which the -n ceiling applies. Must be at least 5. [28]
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kaymccoy
parents:
diff changeset
928 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
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kaymccoy
parents:
diff changeset
929 saturate at 30. This options turns off that rounding. [off]
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kaymccoy
parents:
diff changeset
930 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
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kaymccoy
parents:
diff changeset
931 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
932 with at most INT mismatches. [off]
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kaymccoy
parents:
diff changeset
933 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
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kaymccoy
parents:
diff changeset
934 Does checking on untrimmed reads if -5 or -3 is used. [0]
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kaymccoy
parents:
diff changeset
935 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
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kaymccoy
parents:
diff changeset
936 Does checking on untrimmed reads if -5 or -3 is used. [250]
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kaymccoy
parents:
diff changeset
937 --fr Mate orientation. The upstream/downstream mate orientations for a valid
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kaymccoy
parents:
diff changeset
938 paired-end alignment against the forward reference strand. [--fr]
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kaymccoy
parents:
diff changeset
939 --rf Mate orientation. [off]
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kaymccoy
parents:
diff changeset
940 --ff Mate orientation. [off]
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kaymccoy
parents:
diff changeset
941 --pairtries INT Maximum alignment attempts for paired-end data. [100]
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kaymccoy
parents:
diff changeset
942 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
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kaymccoy
parents:
diff changeset
943 to align against the forward reference strand. [off]
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kaymccoy
parents:
diff changeset
944 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
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kaymccoy
parents:
diff changeset
945 attempt to align against the reverse-complement reference strand. [off]
e28f8c08e736 Uploaded
kaymccoy
parents:
diff changeset
946 --un FILENAME Write all reads that could not be aligned to file [off]
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kaymccoy
parents:
diff changeset
947 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
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kaymccoy
parents:
diff changeset
948 set with the -m option to file [off]
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kaymccoy
parents:
diff changeset
949 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
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kaymccoy
parents:
diff changeset
950 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
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kaymccoy
parents:
diff changeset
951 -y Try hard. Try as hard as possible to find valid alignments when they exist,
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kaymccoy
parents:
diff changeset
952 including paired-end alignments. [off]
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kaymccoy
parents:
diff changeset
953 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
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kaymccoy
parents:
diff changeset
954 store path descriptors in --best mode. [32]
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kaymccoy
parents:
diff changeset
955 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
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kaymccoy
parents:
diff changeset
956 -a All valid alignments. Choosing this means that all valid alignments per read
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kaymccoy
parents:
diff changeset
957 or pair will be reported. [off]
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kaymccoy
parents:
diff changeset
958 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
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kaymccoy
parents:
diff changeset
959 if more than INT reportable alignments exist for it. [no limit]
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kaymccoy
parents:
diff changeset
960 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
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kaymccoy
parents:
diff changeset
961 "best" in terms of stratum (the number of mismatches) and quality values at
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kaymccoy
parents:
diff changeset
962 mismatched position. [off]
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kaymccoy
parents:
diff changeset
963 --strata Best strata. When running in best mode, report alignments that fall into the
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kaymccoy
parents:
diff changeset
964 best stratum if there are ones falling into more than one. [off]
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kaymccoy
parents:
diff changeset
965 -o INT Offrate override. Override the offrate of the index with INT. Some row
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kaymccoy
parents:
diff changeset
966 markings are discarded when index read into memory. INT must be greater than
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kaymccoy
parents:
diff changeset
967 the value used to build the index (default: 5). [off]
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kaymccoy
parents:
diff changeset
968 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
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kaymccoy
parents:
diff changeset
969 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
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kaymccoy
parents:
diff changeset
970 SNPs per base in the subject genome. [see --snpfrac]
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kaymccoy
parents:
diff changeset
971 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
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kaymccoy
parents:
diff changeset
972 alignments. [0.001]
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kaymccoy
parents:
diff changeset
973 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
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kaymccoy
parents:
diff changeset
974 alignments. [off]
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kaymccoy
parents:
diff changeset
975
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kaymccoy
parents:
diff changeset
976 </help>
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kaymccoy
parents:
diff changeset
977 </tool>