annotate bowtie_transcriptome_wrapper_ALLA2/bowtie_transcriptomic_wrapper_test.xml @ 4:b34484a03c12 draft

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author triasteran
date Mon, 13 Feb 2023 10:29:44 +0000
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children b6706d595db8
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1 <tool id="bowtie_trans_wrapper4" name="Bowtie Transcriptome Alignment test ref version" version="1a">
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2 <description>Align to Transcriptome using Bowtie</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0">bowtie</requirement>
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5 <requirement type="package" version="1.13">samtools</requirement>
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6
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7 </requirements>
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8 <version_command>bowtie --version</version_command>
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9 <command>
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10 python '$__tool_directory__/bowtie_transcriptome_wrapper.py'
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11 ## Set number of threads
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12 --threads="\${GALAXY_SLOTS:-4}"
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13 ## Outputs
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14 --output="${output}"
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15 #if str( $singlePaired.sPaired ) == "single"
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16 #if $output_unmapped_reads_l
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17 --output_unmapped_reads="${output_unmapped_reads_l}"
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18 #end if
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19 #if $output_suppressed_reads_l
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20 --output_suppressed_reads="${output_suppressed_reads_l}"
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21 #end if
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22 --galaxy_input_format="${singlePaired.sInput1.ext}"
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23 #else
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24 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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25 --output_unmapped_reads_l="${output_unmapped_reads_l}"
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26 --output_unmapped_reads_r="${output_unmapped_reads_r}"
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27 #end if
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28 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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29 --output_suppressed_reads_l="${output_suppressed_reads_l}"
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30 --output_suppressed_reads_r="${output_suppressed_reads_r}"
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31 #end if
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32 --galaxy_input_format="${singlePaired.pInput1.ext}"
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33 #end if
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34 ## Inputs
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35 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
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36 --suppressHeader="${suppressHeader}"
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37 --genomeSource="${refGenomeSource.genomeSource}"
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38 #if $refGenomeSource.genomeSource == "history":
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39 ##index already exists
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40 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
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41 ##user previously built
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42 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
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43 --do_not_build_index
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44 #else:
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45 ##build index on the fly
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46 --ref="${refGenomeSource.ownFile}"
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47 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
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48 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
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49 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
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50 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
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51 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
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52 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
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53 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
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54 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
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55 #end if
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56 --inodc="${refGenomeSource.indexParams.nodc}"
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57 --inoref="${refGenomeSource.indexParams.noref}"
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58 --ioffrate="${refGenomeSource.indexParams.offrate}"
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59 --iftab="${refGenomeSource.indexParams.ftab}"
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60 --intoa="${refGenomeSource.indexParams.ntoa}"
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61 --iendian="${refGenomeSource.indexParams.endian}"
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62 --iseed="${refGenomeSource.indexParams.seed}"
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63 #end if
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64 #end if
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65 #else
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66 ##use pre-built index
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67 --ref="${refGenomeSource.index.fields.path}"
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68 #end if
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69 --paired="${singlePaired.sPaired}"
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70 #if $singlePaired.sPaired == "single":
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71 --input1="${singlePaired.sInput1}"
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72 --params="${singlePaired.sParams.sSettingsType}"
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73 #if $singlePaired.sParams.sSettingsType == "full":
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74 --skip="${singlePaired.sParams.sSkip}"
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75 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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76 --trimH="${singlePaired.sParams.sTrimH}"
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77 --trimL="${singlePaired.sParams.sTrimL}"
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78 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
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79 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
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80 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
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81 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
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82 --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
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83 #else
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84 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
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85 #end if
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86 --forwardAlign="${singlePaired.sParams.sForwardAlign}"
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87 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
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88 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
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89 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
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90 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
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91 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
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92 #end if
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93 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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94 --best="${singlePaired.sParams.sBestOption.sBest}"
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95 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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96 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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97 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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98 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
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99 #end if
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100 #else:
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101 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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102 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
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103 #end if
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104 #end if
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105 --offrate="${singlePaired.sParams.sOffrate}"
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106 --seed="${singlePaired.sParams.sSeed}"
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107 #end if
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108 #else:
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109 --input1="${singlePaired.pInput1}"
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110 --input2="${singlePaired.pInput2}"
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111 --maxInsert="${singlePaired.pMaxInsert}"
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112 --mateOrient="${singlePaired.pMateOrient}"
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113 --params="${singlePaired.pParams.pSettingsType}"
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114 #if $singlePaired.pParams.pSettingsType == "full":
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115 --skip="${singlePaired.pParams.pSkip}"
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116 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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117 --trimH="${singlePaired.pParams.pTrimH}"
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118 --trimL="${singlePaired.pParams.pTrimL}"
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119 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
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120 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
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121 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
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122 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
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123 --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
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124 #else
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125 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
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126 #end if
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127 --minInsert="${singlePaired.pParams.pMinInsert}"
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128 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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129 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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130 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
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131 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
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132 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
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133 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
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134 #end if
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135 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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136 --best="${singlePaired.pParams.pBestOption.pBest}"
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137 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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138 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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139 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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140 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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141 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
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142 #end if
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143 #else:
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144 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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145 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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146 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
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147 #end if
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148 #end if
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149 --offrate="${singlePaired.pParams.pOffrate}"
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150 --seed="${singlePaired.pParams.pSeed}"
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151 #end if
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152 #end if
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153 #if $save_mapping_stats
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154 --output_mapping_stats="$mapping_stats"
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155 #end if
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156 </command>
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157 <inputs>
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158 <conditional name="refGenomeSource">
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159 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in index?" help="Built-ins were indexed using default options">
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160 <option value="indexed">Use a built-in index</option>
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161 <option value="history">Use one from the history</option>
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162 </param>
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163 <when value="indexed">
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164 <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
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165 <options from_data_table="bowtie_transcriptome_indexes_4">
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166 <filter type="sort_by" column="2" />
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167 <validator type="no_options" message="No indexes are available" />
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168 </options>
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169 </param>
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170 </when>
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171 <when value="history">
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172 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference" />
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173 <conditional name="indexParams">
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174 <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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175 <option value="indexPreSet">Default</option>
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176 <option value="indexFull">Set your own</option>
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177 </param>
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178 <when value="indexPreSet" />
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179 <when value="indexFull">
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180 <conditional name="autoBehavior">
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181 <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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182 <option value="auto">Automatic behavior</option>
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183 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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184 </param>
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185 <when value="auto" />
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186 <when value="set">
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187 <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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188 <option value="unpacked">Use regular representation</option>
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189 <option value="packed">Use packed representation</option>
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190 </param>
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191 <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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192 <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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193 <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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194 </when>
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195 </conditional>
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196 <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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197 <option value="dc">Use difference-cover sample</option>
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parents:
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198 <option value="nodc">Disable difference-cover sample</option>
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199 </param>
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200 <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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parents:
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201 <option value="ref">Build all index files</option>
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parents:
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202 <option value="noref">Do not build paired-end alignment index files</option>
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203 </param>
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204 <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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205 <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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206 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
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parents:
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207 <option value="no">Do not convert Ns</option>
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208 <option value="yes">Convert Ns to As</option>
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209 </param>
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210 <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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211 <option value="little">Little</option>
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parents:
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212 <option value="big">Big</option>
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213 </param>
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214 <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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215 </when> <!-- indexFull -->
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parents:
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216 </conditional> <!-- indexParams -->
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triasteran
parents:
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217 </when> <!-- history -->
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triasteran
parents:
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218 </conditional> <!-- refGenomeSource -->
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triasteran
parents:
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219 <conditional name="singlePaired">
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220 <param name="sPaired" type="select" label="Is this library mate-paired?">
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221 <option value="single">Single-end</option>
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222 <option value="paired">Paired-end</option>
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223 </param>
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224 <when value="single">
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225 <param name="sInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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226 <conditional name="sParams">
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227 <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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228 <option value="preSet">Commonly used</option>
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229 <option value="full" selected="true">Full parameter list</option>
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230 </param>
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parents:
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231 <when value="preSet" />
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parents:
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232 <when value="full">
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parents:
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233 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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234 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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235 <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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236 <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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237 <conditional name="alignModeOption">
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238 <param name="alignMode" type="select" label="Alignment mode">
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parents:
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239 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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240 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
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241 </param>
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242 <when value="nMode">
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243 <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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244 <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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245 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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246 <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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247 <option value="round">Round to nearest 10</option>
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parents:
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248 <option value="noRound">Do not round to nearest 10</option>
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249 </param>
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250 </when>
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251 <when value="vMode">
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252 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
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253 <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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254 </when>
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255 </conditional>
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256 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
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parents:
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257 <option value="forward">Align against the forward reference strand</option>
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parents:
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258 <option value="noForward">Do not align against the forward reference strand</option>
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259 </param>
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260 <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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parents:
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261 <option value="reverse">Align against the reverse-complement reference strand</option>
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parents:
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262 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
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263 </param>
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264 <conditional name="sBestOption">
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265 <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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266 <option value="noBest">Do not use best</option>
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267 <option value="doBest">Use best</option>
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triasteran
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268 </param>
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269 <when value="noBest">
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270 <conditional name="sTryHardOption">
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271 <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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272 <option value="noTryHard">Do not try hard</option>
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273 <option value="doTryHard">Try hard</option>
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274 </param>
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275 <when value="noTryHard">
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276 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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277 </when>
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triasteran
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278 <when value="doTryHard" />
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279 </conditional>
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280 </when>
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281 <when value="doBest">
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282 <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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283 <option value="noStrata">Do not use strata option</option>
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284 <option value="doStrata">Use strata option</option>
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triasteran
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285 </param>
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286 <conditional name="sTryHardOption">
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287 <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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parents:
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288 <option value="noTryHard">Do not try hard</option>
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289 <option value="doTryHard">Try hard</option>
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290 </param>
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291 <when value="noTryHard">
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292 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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293 </when>
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triasteran
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294 <when value="doTryHard" />
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295 </conditional>
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296 </when>
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297 </conditional> <!-- bestOption -->
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298 <conditional name="sAllValAlignsOption">
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299 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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300 <option value="noAllValAligns">Do not report all valid alignments</option>
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301 <option value="doAllValAligns" selected="true">Report all valid alignments</option>
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302 </param>
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303 <when value="noAllValAligns">
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304 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
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305 </when>
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306 <when value="doAllValAligns" />
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307 </conditional>
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308 <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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309 <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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310 <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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311 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
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312 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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313 </when> <!-- full -->
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314 </conditional> <!-- sParams -->
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315 </when> <!-- single -->
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316 <when value="paired">
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317 <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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318 <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
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319 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
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320 <column name="name" index="0"/>
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321 <column name="value" index="0"/>
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322 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
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323 </options>
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324 </param>
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325 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
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326 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
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327 <option value="fr">FR (for Illumina)</option>
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328 <option value="rf">RF</option>
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329 <option value="ff">FF (for SOLiD)</option>
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330 </param>
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331 <conditional name="pParams">
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332 <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
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333 <option value="preSet">Commonly used</option>
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334 <option value="full">Full parameter list</option>
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335 </param>
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336 <when value="preSet" />
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337 <when value="full">
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338 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
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339 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
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340 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
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341 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
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342 <conditional name="alignModeOption">
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parents:
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343 <param name="alignMode" type="select" label="Alignment mode">
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344 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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345 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
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346 </param>
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347 <when value="nMode">
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348 <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" />
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349 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
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350 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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351 <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">
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diff changeset
352 <option value="round">Round to nearest 10</option>
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parents:
diff changeset
353 <option value="noRound">Do not round to nearest 10</option>
b34484a03c12 Uploaded
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parents:
diff changeset
354 </param>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
355 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
356 <when value="vMode">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
357 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
b34484a03c12 Uploaded
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parents:
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358 <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
b34484a03c12 Uploaded
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parents:
diff changeset
359 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
360 </conditional>
b34484a03c12 Uploaded
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parents:
diff changeset
361 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
b34484a03c12 Uploaded
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parents:
diff changeset
362 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
b34484a03c12 Uploaded
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parents:
diff changeset
363 <option value="forward">Align against the forward reference strand</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
364 <option value="noForward">Do not align against the forward reference strand</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
365 </param>
b34484a03c12 Uploaded
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parents:
diff changeset
366 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
b34484a03c12 Uploaded
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parents:
diff changeset
367 <option value="reverse">Align against the reverse-complement reference strand</option>
b34484a03c12 Uploaded
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parents:
diff changeset
368 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
b34484a03c12 Uploaded
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parents:
diff changeset
369 </param>
b34484a03c12 Uploaded
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parents:
diff changeset
370 <conditional name="pBestOption">
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parents:
diff changeset
371 <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">
b34484a03c12 Uploaded
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parents:
diff changeset
372 <option value="noBest">Do not use best</option>
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triasteran
parents:
diff changeset
373 <option value="doBest">Use best</option>
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triasteran
parents:
diff changeset
374 </param>
b34484a03c12 Uploaded
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parents:
diff changeset
375 <when value="noBest">
b34484a03c12 Uploaded
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parents:
diff changeset
376 <conditional name="pTryHardOption">
b34484a03c12 Uploaded
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parents:
diff changeset
377 <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">
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parents:
diff changeset
378 <option value="noTryHard">Do not try hard</option>
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triasteran
parents:
diff changeset
379 <option value="doTryHard">Try hard</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
380 </param>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
381 <when value="noTryHard">
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parents:
diff changeset
382 <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)" />
b34484a03c12 Uploaded
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parents:
diff changeset
383 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
384 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
385 <when value="doTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
386 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
387 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
388 <when value="doBest">
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parents:
diff changeset
389 <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)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
390 <option value="noStrata">Do not use strata option</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
391 <option value="doStrata">Use strata option</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
392 </param>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
393 <conditional name="pTryHardOption">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
394 <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">
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parents:
diff changeset
395 <option value="noTryHard">Do not try hard</option>
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triasteran
parents:
diff changeset
396 <option value="doTryHard">Try hard</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
397 </param>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
398 <when value="noTryHard">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
399 <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)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
400 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
401 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
402 <when value="doTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
403 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
404 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
405 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
406 <conditional name="pAllValAlignsOption">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
407 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
408 <option value="noAllValAligns">Do not report all valid alignments</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
409 <option value="doAllValAligns">Report all valid alignments</option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
410 </param>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
411 <when value="noAllValAligns">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
412 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
413 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
414 <when value="doAllValAligns" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
415 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
416 <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" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
417 <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)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
418 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
419 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
420 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
421 </when> <!-- full -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
422 </conditional> <!-- pParams -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
423 </when> <!-- paired -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
424 </conditional> <!-- singlePaired -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
425 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
426 <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" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
427 </inputs>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
428 <outputs>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
429 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
430 <actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
431 <conditional name="refGenomeSource.genomeSource">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
432 <when value="indexed">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
433 <action type="metadata" name="dbkey">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
434 <option type="from_data_table" name="bowtie_transcriptome_indexes_4" column="1" offset="0">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
435 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
436 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
437 </option>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
438 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
439 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
440 <when value="history">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
441 <action type="metadata" name="dbkey">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
442 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
443 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
444 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
445 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
446 </actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
447 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
448 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
449 <filter>save_mapping_stats is True</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
450 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
451 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
452 <filter>((
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
453 singlePaired['sPaired'] == "single" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
454 singlePaired['sParams']['sSettingsType'] == "full" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
455 singlePaired['sParams']['sMaxFile'] is True
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
456 ) or (
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
457 singlePaired['sPaired'] == "paired" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
458 singlePaired['pParams']['pSettingsType'] == "full" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
459 singlePaired['pParams']['pMaxFile'] is True
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
460 ))
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
461 </filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
462 <actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
463 <conditional name="singlePaired.sPaired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
464 <when value="single">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
465 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
466 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
467 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
468 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
469 <when value="paired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
470 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
471 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
472 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
473 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
474 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
475 </actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
476 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
477 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
478 <filter>singlePaired['sPaired'] == "paired"</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
479 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
480 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
481 <actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
482 <conditional name="singlePaired.sPaired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
483 <when value="single">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
484 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
485 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
486 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
487 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
488 <when value="paired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
489 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
490 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
491 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
492 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
493 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
494 </actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
495 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
496 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
497 <filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
498 ((
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
499 singlePaired['sPaired'] == "single" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
500 singlePaired['sParams']['sSettingsType'] == "full" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
501 singlePaired['sParams']['sUnmappedFile'] is True
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
502 ) or (
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
503 singlePaired['sPaired'] == "paired" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
504 singlePaired['pParams']['pSettingsType'] == "full" and
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
505 singlePaired['pParams']['pUnmappedFile'] is True
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
506 ))
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
507 </filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
508 <actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
509 <conditional name="singlePaired.sPaired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
510 <when value="single">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
511 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
512 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
513 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
514 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
515 <when value="paired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
516 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
517 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
518 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
519 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
520 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
521 </actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
522 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
523 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
524 <filter>singlePaired['sPaired'] == "paired"</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
525 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
526 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
527 <actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
528 <conditional name="singlePaired.sPaired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
529 <when value="single">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
530 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
531 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
532 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
533 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
534 <when value="paired">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
535 <action type="format">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
536 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
537 </action>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
538 </when>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
539 </conditional>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
540 </actions>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
541 </data>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
542 </outputs>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
543 <tests>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
544 <test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
545 <!--
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
546 Bowtie command:
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
547 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
548 sort bowtie_out6_u.sam > bowtie_out6.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
549 -p is the number of threads. You need to replace the + with 2 dashes.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
550 chrM_base needs to be the base location/name of the index files.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
551 -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
552 <param name="genomeSource" value="indexed" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
553 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
554 <param name="index" value="equCab2chrM" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
555 <param name="sPaired" value="single" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
556 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
557 <param name="sSettingsType" value="preSet" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
558 <param name="suppressHeader" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
559 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
560 <metadata name="dbkey" value="equCab2" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
561 </output>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
562 </test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
563 <test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
564 <!--
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
565 Bowtie command:
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
566 bowtie-build -f test-data/phiX.fasta phiX_base
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
567 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
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
568 sort bowtie_out7_u.sam > bowtie_out7.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
569 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
570 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
571 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
572 -p is the number of threads. You need to replace the + with 2 dashes.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
573 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
574 chrM_base is the index files' location/base name.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
575 -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
576 <param name="genomeSource" value="history" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
577 <param name="ownFile" value="phiX.fasta" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
578 <param name="indexSettings" value="indexPreSet" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
579 <param name="sPaired" value="paired" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
580 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
581 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
582 <param name="pMaxInsert" value="1000" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
583 <param name="pMateOrient" value="ff" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
584 <param name="pSettingsType" value="full" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
585 <param name="pSkip" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
586 <param name="pAlignLimit" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
587 <param name="pTrimH" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
588 <param name="pTrimL" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
589 <param name="alignMode" value="nMode" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
590 <param name="pMismatchSeed" value="2" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
591 <param name="pMismatchQual" value="70" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
592 <param name="pSeedLen" value="28" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
593 <param name="pRounding" value="round" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
594 <param name="pMinInsert" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
595 <param name="pMaxAlignAttempt" value="100" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
596 <param name="pForwardAlign" value="forward" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
597 <param name="pReverseAlign" value="reverse" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
598 <param name="pTryHard" value="noTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
599 <param name="pValAlign" value="1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
600 <param name="pAllValAligns" value="noAllValAligns" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
601 <param name="pSuppressAlign" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
602 <param name="pUnmappedFile" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
603 <param name="pMaxFile" value="false" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
604 <param name="pBest" value="doBest" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
605 <param name="pdMaxBacktracks" value="800" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
606 <param name="pdStrata" value="noStrata" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
607 <param name="pOffrate" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
608 <param name="pSeed" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
609 <param name="suppressHeader" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
610 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
611 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
612 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
613 </test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
614 <!-- start testing of non-sanger variant fastq reads -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
615 <test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
616 <param name="genomeSource" value="history" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
617 <param name="ownFile" value="phiX.fasta" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
618 <param name="indexSettings" value="indexPreSet" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
619 <param name="sPaired" value="paired" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
620 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
621 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
622 <param name="pMaxInsert" value="1000" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
623 <param name="pMateOrient" value="ff" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
624 <param name="pSettingsType" value="full" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
625 <param name="pSkip" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
626 <param name="pAlignLimit" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
627 <param name="pTrimH" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
628 <param name="pTrimL" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
629 <param name="alignMode" value="nMode" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
630 <param name="pMismatchSeed" value="2" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
631 <param name="pMismatchQual" value="70" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
632 <param name="pSeedLen" value="28" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
633 <param name="pRounding" value="round" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
634 <param name="pMinInsert" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
635 <param name="pMaxAlignAttempt" value="100" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
636 <param name="pForwardAlign" value="forward" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
637 <param name="pReverseAlign" value="reverse" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
638 <param name="pTryHard" value="noTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
639 <param name="pValAlign" value="1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
640 <param name="pAllValAligns" value="noAllValAligns" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
641 <param name="pSuppressAlign" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
642 <param name="pUnmappedFile" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
643 <param name="pMaxFile" value="false" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
644 <param name="pBest" value="doBest" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
645 <param name="pdMaxBacktracks" value="800" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
646 <param name="pdStrata" value="noStrata" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
647 <param name="pOffrate" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
648 <param name="pSeed" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
649 <param name="suppressHeader" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
650 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
651 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
652 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
653 </test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
654 <test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
655 <param name="genomeSource" value="history" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
656 <param name="ownFile" value="phiX.fasta" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
657 <param name="indexSettings" value="indexPreSet" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
658 <param name="sPaired" value="paired" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
659 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
660 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
661 <param name="pMaxInsert" value="1000" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
662 <param name="pMateOrient" value="ff" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
663 <param name="pSettingsType" value="full" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
664 <param name="pSkip" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
665 <param name="pAlignLimit" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
666 <param name="pTrimH" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
667 <param name="pTrimL" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
668 <param name="alignMode" value="nMode" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
669 <param name="pMismatchSeed" value="2" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
670 <param name="pMismatchQual" value="70" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
671 <param name="pSeedLen" value="28" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
672 <param name="pRounding" value="round" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
673 <param name="pMinInsert" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
674 <param name="pMaxAlignAttempt" value="100" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
675 <param name="pForwardAlign" value="forward" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
676 <param name="pReverseAlign" value="reverse" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
677 <param name="pTryHard" value="noTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
678 <param name="pValAlign" value="1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
679 <param name="pAllValAligns" value="noAllValAligns" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
680 <param name="pSuppressAlign" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
681 <param name="pUnmappedFile" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
682 <param name="pMaxFile" value="false" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
683 <param name="pBest" value="doBest" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
684 <param name="pdMaxBacktracks" value="800" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
685 <param name="pdStrata" value="noStrata" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
686 <param name="pOffrate" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
687 <param name="pSeed" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
688 <param name="suppressHeader" value="true" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
689 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
690 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
691 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
692 </test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
693 <!-- end testing of non-sanger variant fastq reads -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
694 <test>
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
695 <!--
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
696 Bowtie command:
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
697 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
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
698 sort bowtie_out9_u.sam > bowtie_out9.sam
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
699 -p is the number of threads. You need to replace the + with 2 dashes.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
700 chrM_base is the index files' location/base name.
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
701 -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
702 <param name="genomeSource" value="indexed" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
703 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
704 <param name="index" value="equCab2chrM" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
705 <param name="sPaired" value="single" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
706 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
707 <param name="sSettingsType" value="full" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
708 <param name="sSkip" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
709 <param name="sAlignLimit" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
710 <param name="sTrimH" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
711 <param name="sTrimL" value="0" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
712 <param name="alignMode" value="nMode" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
713 <param name="sMismatchSeed" value="2" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
714 <param name="sMismatchQual" value="70" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
715 <param name="sSeedLen" value="28" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
716 <param name="sRounding" value="round" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
717 <param name="sForwardAlign" value="forward" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
718 <param name="sReverseAlign" value="reverse" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
719 <param name="sTryHard" value="doTryHard" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
720 <param name="sValAlign" value="1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
721 <param name="sAllValAligns" value="noAllValAligns" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
722 <param name="sSuppressAlign" value="-1" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
723 <param name="sUnmappedFile" value="false" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
724 <param name="sMaxFile" value="false" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
725 <param name="sBest" value="noBest" />
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
726 <param name="sOffrate" value="-1" />
b34484a03c12 Uploaded
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parents:
diff changeset
727 <param name="sSeed" value="-1" />
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triasteran
parents:
diff changeset
728 <param name="suppressHeader" value="true" />
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parents:
diff changeset
729 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
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triasteran
parents:
diff changeset
730 <metadata name="dbkey" value="equCab2" />
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triasteran
parents:
diff changeset
731 </output>
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triasteran
parents:
diff changeset
732 </test>
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triasteran
parents:
diff changeset
733 <test>
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triasteran
parents:
diff changeset
734 <!--
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triasteran
parents:
diff changeset
735 Bowtie command:
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parents:
diff changeset
736 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
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parents:
diff changeset
737 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
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triasteran
parents:
diff changeset
738 sort bowtie_out10_u.sam > bowtie_out10.sam
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triasteran
parents:
diff changeset
739 -p is the number of threads. You need to replace the + with 2 dashes.
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triasteran
parents:
diff changeset
740 chrM_base is the index files' location/base name.
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triasteran
parents:
diff changeset
741 -->
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triasteran
parents:
diff changeset
742 <param name="genomeSource" value="history" />
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triasteran
parents:
diff changeset
743 <param name="ownFile" value="phiX.fasta" />
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triasteran
parents:
diff changeset
744 <param name="indexSettings" value="indexFull" />
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triasteran
parents:
diff changeset
745 <param name="autoB" value="auto" />
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triasteran
parents:
diff changeset
746 <param name="nodc" value="dc" />
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triasteran
parents:
diff changeset
747 <param name="noref" value="ref" />
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triasteran
parents:
diff changeset
748 <param name="offrate" value="5" />
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triasteran
parents:
diff changeset
749 <param name="ftab" value="10" />
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triasteran
parents:
diff changeset
750 <param name="ntoa" value="no" />
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triasteran
parents:
diff changeset
751 <param name="endian" value="little" />
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triasteran
parents:
diff changeset
752 <param name="seed" value="-1" />
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triasteran
parents:
diff changeset
753 <param name="sPaired" value="paired" />
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triasteran
parents:
diff changeset
754 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
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triasteran
parents:
diff changeset
755 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
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triasteran
parents:
diff changeset
756 <param name="pMaxInsert" value="1000" />
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triasteran
parents:
diff changeset
757 <param name="pMateOrient" value="ff" />
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triasteran
parents:
diff changeset
758 <param name="pSettingsType" value="preSet" />
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triasteran
parents:
diff changeset
759 <param name="suppressHeader" value="true" />
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triasteran
parents:
diff changeset
760 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
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triasteran
parents:
diff changeset
761 </test>
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triasteran
parents:
diff changeset
762 <test>
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triasteran
parents:
diff changeset
763 <!--
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
764 Bowtie command:
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
765 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
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parents:
diff changeset
766 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
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triasteran
parents:
diff changeset
767 sort bowtie_out10_u.sam > bowtie_out10.sam
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triasteran
parents:
diff changeset
768 -p is the number of threads. You need to replace the + with 2 dashes.
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triasteran
parents:
diff changeset
769 chrM_base is the index files' location/base name.
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triasteran
parents:
diff changeset
770 -->
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triasteran
parents:
diff changeset
771 <param name="genomeSource" value="history" />
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triasteran
parents:
diff changeset
772 <param name="ownFile" value="phiX.fasta" />
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triasteran
parents:
diff changeset
773 <param name="indexSettings" value="indexFull" />
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triasteran
parents:
diff changeset
774 <param name="autoB" value="auto" />
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triasteran
parents:
diff changeset
775 <param name="nodc" value="dc" />
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triasteran
parents:
diff changeset
776 <param name="noref" value="ref" />
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triasteran
parents:
diff changeset
777 <param name="offrate" value="5" />
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triasteran
parents:
diff changeset
778 <param name="ftab" value="10" />
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triasteran
parents:
diff changeset
779 <param name="ntoa" value="no" />
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triasteran
parents:
diff changeset
780 <param name="endian" value="little" />
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triasteran
parents:
diff changeset
781 <param name="seed" value="-1" />
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triasteran
parents:
diff changeset
782 <param name="sPaired" value="paired" />
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triasteran
parents:
diff changeset
783 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
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triasteran
parents:
diff changeset
784 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
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triasteran
parents:
diff changeset
785 <param name="pMaxInsert" value="1000" />
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triasteran
parents:
diff changeset
786 <param name="pMateOrient" value="ff" />
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triasteran
parents:
diff changeset
787 <param name="pSettingsType" value="preSet" />
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triasteran
parents:
diff changeset
788 <param name="suppressHeader" value="true" />
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triasteran
parents:
diff changeset
789 <param name="save_mapping_stats" value="true" />
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triasteran
parents:
diff changeset
790 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
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triasteran
parents:
diff changeset
791 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
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triasteran
parents:
diff changeset
792 </test>
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triasteran
parents:
diff changeset
793 </tests>
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triasteran
parents:
diff changeset
794
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
795 <help>
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triasteran
parents:
diff changeset
796
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triasteran
parents:
diff changeset
797 **What it does**
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parents:
diff changeset
798
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triasteran
parents:
diff changeset
799 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.
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triasteran
parents:
diff changeset
800
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triasteran
parents:
diff changeset
801 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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triasteran
parents:
diff changeset
802
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triasteran
parents:
diff changeset
803 ------
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
804
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triasteran
parents:
diff changeset
805 **Know what you are doing**
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triasteran
parents:
diff changeset
806
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triasteran
parents:
diff changeset
807 .. class:: warningmark
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parents:
diff changeset
808
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triasteran
parents:
diff changeset
809 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.
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parents:
diff changeset
810
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triasteran
parents:
diff changeset
811 .. __: http://bowtie-bio.sourceforge.net/index.shtml
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triasteran
parents:
diff changeset
812
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triasteran
parents:
diff changeset
813 ------
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triasteran
parents:
diff changeset
814
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
815 **Input formats**
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parents:
diff changeset
816
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triasteran
parents:
diff changeset
817 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
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triasteran
parents:
diff changeset
818
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
819 ------
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triasteran
parents:
diff changeset
820
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triasteran
parents:
diff changeset
821 **A Note on Built-in Reference Genomes**
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parents:
diff changeset
822
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parents:
diff changeset
823 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.
b34484a03c12 Uploaded
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parents:
diff changeset
824
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
825 ------
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
826
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triasteran
parents:
diff changeset
827 **Outputs**
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parents:
diff changeset
828
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parents:
diff changeset
829 The output is in SAM format, and has the following columns::
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parents:
diff changeset
830
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parents:
diff changeset
831 Column Description
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parents:
diff changeset
832 -------- --------------------------------------------------------
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parents:
diff changeset
833 1 QNAME Query (pair) NAME
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parents:
diff changeset
834 2 FLAG bitwise FLAG
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parents:
diff changeset
835 3 RNAME Reference sequence NAME
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triasteran
parents:
diff changeset
836 4 POS 1-based leftmost POSition/coordinate of clipped sequence
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triasteran
parents:
diff changeset
837 5 MAPQ MAPping Quality (Phred-scaled)
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parents:
diff changeset
838 6 CIGAR extended CIGAR string
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triasteran
parents:
diff changeset
839 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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triasteran
parents:
diff changeset
840 8 MPOS 1-based Mate POSition
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triasteran
parents:
diff changeset
841 9 ISIZE Inferred insert SIZE
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parents:
diff changeset
842 10 SEQ query SEQuence on the same strand as the reference
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triasteran
parents:
diff changeset
843 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
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triasteran
parents:
diff changeset
844 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
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triasteran
parents:
diff changeset
845
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triasteran
parents:
diff changeset
846 The flags are as follows::
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parents:
diff changeset
847
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triasteran
parents:
diff changeset
848 Flag Description
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triasteran
parents:
diff changeset
849 ------ -------------------------------------
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
850 0x0001 the read is paired in sequencing
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triasteran
parents:
diff changeset
851 0x0002 the read is mapped in a proper pair
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triasteran
parents:
diff changeset
852 0x0004 the query sequence itself is unmapped
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triasteran
parents:
diff changeset
853 0x0008 the mate is unmapped
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triasteran
parents:
diff changeset
854 0x0010 strand of the query (1 for reverse)
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triasteran
parents:
diff changeset
855 0x0020 strand of the mate
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
856 0x0040 the read is the first read in a pair
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triasteran
parents:
diff changeset
857 0x0080 the read is the second read in a pair
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triasteran
parents:
diff changeset
858 0x0100 the alignment is not primary
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triasteran
parents:
diff changeset
859
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triasteran
parents:
diff changeset
860 It looks like this (scroll sideways to see the entire example)::
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triasteran
parents:
diff changeset
861
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triasteran
parents:
diff changeset
862 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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parents:
diff changeset
863 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
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triasteran
parents:
diff changeset
864 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
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triasteran
parents:
diff changeset
865
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
866 -------
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triasteran
parents:
diff changeset
867
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triasteran
parents:
diff changeset
868 **Bowtie settings**
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triasteran
parents:
diff changeset
869
b34484a03c12 Uploaded
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parents:
diff changeset
870 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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parents:
diff changeset
871
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triasteran
parents:
diff changeset
872 ------
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triasteran
parents:
diff changeset
873
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triasteran
parents:
diff changeset
874 **Bowtie parameter list**
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parents:
diff changeset
875
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triasteran
parents:
diff changeset
876 This is an exhaustive list of Bowtie options:
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parents:
diff changeset
877
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triasteran
parents:
diff changeset
878 For indexing (bowtie-build)::
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triasteran
parents:
diff changeset
879
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parents:
diff changeset
880 -a No auto behavior. Disable the default behavior where bowtie automatically
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
881 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
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triasteran
parents:
diff changeset
882 to the memory available. [off]
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parents:
diff changeset
883 --packed Packing. Use a packed representation for DNA strings. [auto]
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triasteran
parents:
diff changeset
884 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
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triasteran
parents:
diff changeset
885 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
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triasteran
parents:
diff changeset
886 expressed as a fraction of the length of the reference. [4]
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triasteran
parents:
diff changeset
887 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
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triasteran
parents:
diff changeset
888 sample. [1024]
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triasteran
parents:
diff changeset
889 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
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triasteran
parents:
diff changeset
890 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
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triasteran
parents:
diff changeset
891 of the index. Used only for paired-end alignment. [off]
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triasteran
parents:
diff changeset
892 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
893 indexer will mark every 2^INT rows. The marked rows correspond to rows on
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
894 the genome. [5]
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parents:
diff changeset
895 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
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triasteran
parents:
diff changeset
896 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
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parents:
diff changeset
897 bytes. [10]
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triasteran
parents:
diff changeset
898 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
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triasteran
parents:
diff changeset
899 simply excluded from the index and Bowtie will not find alignments that
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parents:
diff changeset
900 overlap them. [off]
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parents:
diff changeset
901 --big Endianness. Endianness to use when serializing integers to the index file. [off]
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parents:
diff changeset
902 --little Endianness. [--little]
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parents:
diff changeset
903 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
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parents:
diff changeset
904
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triasteran
parents:
diff changeset
905 For aligning (bowtie)::
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parents:
diff changeset
906
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parents:
diff changeset
907 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
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parents:
diff changeset
908 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
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triasteran
parents:
diff changeset
909 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
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triasteran
parents:
diff changeset
910 read before alignment. [0]
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triasteran
parents:
diff changeset
911 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
b34484a03c12 Uploaded
triasteran
parents:
diff changeset
912 read before alignment. [0]
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triasteran
parents:
diff changeset
913 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
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triasteran
parents:
diff changeset
914 with seed length option). Can be 0, 1, 2, or 3. [2]
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parents:
diff changeset
915 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
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triasteran
parents:
diff changeset
916 read positions. Bowtie rounds quality values to the nearest 10 and saturates
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parents:
diff changeset
917 at 30. [70]
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triasteran
parents:
diff changeset
918 -l INT Seed length. The number of bases on the high-quality end of the read to
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919 which the -n ceiling applies. Must be at least 5. [28]
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920 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
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parents:
diff changeset
921 saturate at 30. This options turns off that rounding. [off]
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parents:
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922 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
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triasteran
parents:
diff changeset
923 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
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parents:
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924 with at most INT mismatches. [off]
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925 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
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triasteran
parents:
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926 Does checking on untrimmed reads if -5 or -3 is used. [0]
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parents:
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927 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
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parents:
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928 Does checking on untrimmed reads if -5 or -3 is used. [250]
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parents:
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929 --fr Mate orientation. The upstream/downstream mate orientations for a valid
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triasteran
parents:
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930 paired-end alignment against the forward reference strand. [--fr]
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triasteran
parents:
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931 --rf Mate orientation. [off]
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triasteran
parents:
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932 --ff Mate orientation. [off]
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parents:
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933 --pairtries INT Maximum alignment attempts for paired-end data. [100]
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parents:
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934 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
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parents:
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935 to align against the forward reference strand. [off]
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triasteran
parents:
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936 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
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parents:
diff changeset
937 attempt to align against the reverse-complement reference strand. [off]
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triasteran
parents:
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938 --un FILENAME Write all reads that could not be aligned to file [off]
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triasteran
parents:
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939 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
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parents:
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940 set with the -m option to file [off]
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parents:
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941 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
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triasteran
parents:
diff changeset
942 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
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triasteran
parents:
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943 -y Try hard. Try as hard as possible to find valid alignments when they exist,
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triasteran
parents:
diff changeset
944 including paired-end alignments. [off]
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parents:
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945 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
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triasteran
parents:
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946 store path descriptors in --best mode. [32]
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parents:
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947 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
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triasteran
parents:
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948 -a All valid alignments. Choosing this means that all valid alignments per read
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triasteran
parents:
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949 or pair will be reported. [off]
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parents:
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950 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
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parents:
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951 if more than INT reportable alignments exist for it. [no limit]
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parents:
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952 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
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triasteran
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diff changeset
953 "best" in terms of stratum (the number of mismatches) and quality values at
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triasteran
parents:
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954 mismatched position. [off]
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955 --strata Best strata. When running in best mode, report alignments that fall into the
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triasteran
parents:
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956 best stratum if there are ones falling into more than one. [off]
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parents:
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957 -o INT Offrate override. Override the offrate of the index with INT. Some row
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parents:
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958 markings are discarded when index read into memory. INT must be greater than
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959 the value used to build the index (default: 5). [off]
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960 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
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parents:
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961 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
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parents:
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962 SNPs per base in the subject genome. [see --snpfrac]
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963 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
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parents:
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964 alignments. [0.001]
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parents:
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965 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
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parents:
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966 alignments. [off]
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parents:
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967
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parents:
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968 </help>
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parents:
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969 <citations>
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970 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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parents:
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971 </citations>
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972 </tool>