annotate bowtie_genome_wrapper/bowtie_genomic_wrapper.xml @ 2:7e3bd576aa7c draft default tip

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author triasteran
date Tue, 26 Apr 2022 12:21:05 +0000
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1 <tool id="bowtie_genomic_wrapper" name="Align to the Genome with Bowtie" version="1.3.q">
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2 <description></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 </requirements>
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6 <version_command>bowtie --version</version_command>
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7 <command>
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8 python '$__tool_directory__/bowtie_genomic_wrapper.py'
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9 ## Set number of threads
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10 --threads="\${GALAXY_SLOTS:-4}"
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11 ## Outputs
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12 --output="${output}"
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13 #if str( $singlePaired.sPaired ) == "single"
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14 #if $output_unmapped_reads_l
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15 --output_unmapped_reads="${output_unmapped_reads_l}"
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16 #end if
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17 #if $output_suppressed_reads_l
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18 --output_suppressed_reads="${output_suppressed_reads_l}"
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19 #end if
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20 --galaxy_input_format="${singlePaired.sInput1.ext}"
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21 #else
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22 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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23 --output_unmapped_reads_l="${output_unmapped_reads_l}"
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24 --output_unmapped_reads_r="${output_unmapped_reads_r}"
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25 #end if
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26 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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27 --output_suppressed_reads_l="${output_suppressed_reads_l}"
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28 --output_suppressed_reads_r="${output_suppressed_reads_r}"
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29 #end if
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30 --galaxy_input_format="${singlePaired.pInput1.ext}"
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31 #end if
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32 ## Inputs
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33 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
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34 --suppressHeader="${suppressHeader}"
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35 --genomeSource="${refGenomeSource.genomeSource}"
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36 #if $refGenomeSource.genomeSource == "history":
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37 ##index already exists
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38 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
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39 ##user previously built
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40 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
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41 --do_not_build_index
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42 #else:
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43 ##build index on the fly
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44 --ref="${refGenomeSource.ownFile}"
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45 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
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46 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
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47 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
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48 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
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49 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
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50 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
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51 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
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52 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
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53 #end if
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54 --inodc="${refGenomeSource.indexParams.nodc}"
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55 --inoref="${refGenomeSource.indexParams.noref}"
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56 --ioffrate="${refGenomeSource.indexParams.offrate}"
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57 --iftab="${refGenomeSource.indexParams.ftab}"
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58 --intoa="${refGenomeSource.indexParams.ntoa}"
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59 --iendian="${refGenomeSource.indexParams.endian}"
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60 --iseed="${refGenomeSource.indexParams.seed}"
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61 #end if
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62 #end if
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63 #else
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64 ##use pre-built index
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65 --ref="${refGenomeSource.index.fields.path}"
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66 #end if
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67 --paired="${singlePaired.sPaired}"
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68 #if $singlePaired.sPaired == "single":
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69 --input1="${singlePaired.sInput1}"
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70 --params="${singlePaired.sParams.sSettingsType}"
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71 #if $singlePaired.sParams.sSettingsType == "full":
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72 --skip="${singlePaired.sParams.sSkip}"
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73 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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74 --trimH="${singlePaired.sParams.sTrimH}"
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75 --trimL="${singlePaired.sParams.sTrimL}"
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76 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
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77 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
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78 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
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79 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
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80 --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
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81 #else
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82 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
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83 #end if
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84 --forwardAlign="${singlePaired.sParams.sForwardAlign}"
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85 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
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86 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
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87 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
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88 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
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89 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
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90 #end if
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91 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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92 --best="${singlePaired.sParams.sBestOption.sBest}"
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93 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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94 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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95 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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96 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
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97 #end if
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98 #else:
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99 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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100 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
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101 #end if
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102 #end if
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103 --offrate="${singlePaired.sParams.sOffrate}"
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104 --seed="${singlePaired.sParams.sSeed}"
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105 #end if
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106 #else:
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107 --input1="${singlePaired.pInput1}"
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108 --input2="${singlePaired.pInput2}"
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109 --maxInsert="${singlePaired.pMaxInsert}"
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110 --mateOrient="${singlePaired.pMateOrient}"
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111 --params="${singlePaired.pParams.pSettingsType}"
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112 #if $singlePaired.pParams.pSettingsType == "full":
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113 --skip="${singlePaired.pParams.pSkip}"
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114 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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115 --trimH="${singlePaired.pParams.pTrimH}"
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116 --trimL="${singlePaired.pParams.pTrimL}"
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117 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
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118 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
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119 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
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120 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
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121 --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
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122 #else
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123 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
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124 #end if
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parents:
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125 --minInsert="${singlePaired.pParams.pMinInsert}"
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126 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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127 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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128 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
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129 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
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130 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
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131 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
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132 #end if
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parents:
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133 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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134 --best="${singlePaired.pParams.pBestOption.pBest}"
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135 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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136 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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137 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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138 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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139 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
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140 #end if
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parents:
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141 #else:
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142 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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143 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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144 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
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145 #end if
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parents:
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146 #end if
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parents:
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147 --offrate="${singlePaired.pParams.pOffrate}"
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148 --seed="${singlePaired.pParams.pSeed}"
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parents:
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149 #end if
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parents:
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150 #end if
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parents:
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151 #if $save_mapping_stats
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152 --output_mapping_stats="$mapping_stats"
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153 #end if
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154 </command>
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155 <inputs>
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156 <conditional name="refGenomeSource">
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157 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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158 <option value="indexed">Use a built-in index</option>
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159 <option value="history">Use one from the history</option>
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160 </param>
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161 <when value="indexed">
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162 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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163 <options from_data_table="bowtie_genome_indexes">
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164 <filter type="sort_by" column="2" />
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165 <validator type="no_options" message="No indexes are available" />
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166 </options>
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167 </param>
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168 </when>
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169 <when value="history">
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170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
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171 <conditional name="indexParams">
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172 <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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173 <option value="indexPreSet">Default</option>
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174 <option value="indexFull">Set your own</option>
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175 </param>
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176 <when value="indexPreSet" />
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177 <when value="indexFull">
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178 <conditional name="autoBehavior">
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179 <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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180 <option value="auto">Automatic behavior</option>
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181 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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182 </param>
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183 <when value="auto" />
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184 <when value="set">
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185 <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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186 <option value="unpacked">Use regular representation</option>
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187 <option value="packed">Use packed representation</option>
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188 </param>
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189 <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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190 <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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191 <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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192 </when>
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193 </conditional>
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194 <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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195 <option value="dc">Use difference-cover sample</option>
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196 <option value="nodc">Disable difference-cover sample</option>
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197 </param>
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198 <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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199 <option value="ref">Build all index files</option>
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200 <option value="noref">Do not build paired-end alignment index files</option>
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201 </param>
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202 <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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203 <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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204 <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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205 <option value="no">Do not convert Ns</option>
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206 <option value="yes">Convert Ns to As</option>
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207 </param>
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208 <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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209 <option value="little">Little</option>
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210 <option value="big">Big</option>
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211 </param>
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212 <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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213 </when> <!-- indexFull -->
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214 </conditional> <!-- indexParams -->
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215 </when> <!-- history -->
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216 </conditional> <!-- refGenomeSource -->
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217 <conditional name="singlePaired">
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218 <param name="sPaired" type="select" label="Is this library mate-paired?">
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219 <option value="single">Single-end</option>
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220 <option value="paired">Paired-end</option>
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221 </param>
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222 <when value="single">
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223 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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224 <conditional name="sParams">
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225 <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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226 <option value="preSet">Commonly used</option>
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227 <option value="full" selected="true">Full parameter list</option>
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228 </param>
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229 <when value="preSet" />
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230 <when value="full">
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231 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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232 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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233 <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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234 <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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235 <conditional name="alignModeOption">
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236 <param name="alignMode" type="select" label="Alignment mode">
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parents:
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237 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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238 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
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239 </param>
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240 <when value="nMode">
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241 <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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242 <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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243 <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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244 <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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245 <option value="round">Round to nearest 10</option>
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246 <option value="noRound">Do not round to nearest 10</option>
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247 </param>
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248 </when>
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249 <when value="vMode">
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250 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
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251 </when>
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252 </conditional>
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253 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
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254 <option value="forward">Align against the forward reference strand</option>
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255 <option value="noForward">Do not align against the forward reference strand</option>
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256 </param>
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257 <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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258 <option value="reverse">Align against the reverse-complement reference strand</option>
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259 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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260 </param>
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261 <conditional name="sBestOption">
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262 <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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263 <option value="noBest">Do not use best</option>
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264 <option value="doBest">Use best</option>
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265 </param>
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266 <when value="noBest">
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267 <conditional name="sTryHardOption">
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268 <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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269 <option value="noTryHard">Do not try hard</option>
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270 <option value="doTryHard">Try hard</option>
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271 </param>
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272 <when value="noTryHard">
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273 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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274 </when>
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275 <when value="doTryHard" />
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276 </conditional>
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277 </when>
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278 <when value="doBest">
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279 <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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280 <option value="noStrata">Do not use strata option</option>
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281 <option value="doStrata">Use strata option</option>
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282 </param>
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283 <conditional name="sTryHardOption">
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284 <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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285 <option value="noTryHard">Do not try hard</option>
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286 <option value="doTryHard">Try hard</option>
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287 </param>
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288 <when value="noTryHard">
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289 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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290 </when>
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291 <when value="doTryHard" />
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292 </conditional>
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293 </when>
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294 </conditional> <!-- bestOption -->
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295 <conditional name="sAllValAlignsOption">
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296 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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297 <option value="noAllValAligns">Do not report all valid alignments</option>
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298 <option value="doAllValAligns">Report all valid alignments</option>
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299 </param>
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300 <when value="noAllValAligns">
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301 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
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302 </when>
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303 <when value="doAllValAligns" />
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304 </conditional>
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305 <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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306 <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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307 <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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308 <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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309 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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310 </when> <!-- full -->
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311 </conditional> <!-- sParams -->
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312 </when> <!-- single -->
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313 <when value="paired">
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314 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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315 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
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316 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
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317 <column name="name" index="0"/>
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318 <column name="value" index="0"/>
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319 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
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320 </options>
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321 </param>
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322 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
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323 <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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324 <option value="fr">FR (for Illumina)</option>
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325 <option value="rf">RF</option>
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326 <option value="ff">FF (for SOLiD)</option>
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327 </param>
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328 <conditional name="pParams">
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329 <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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330 <option value="preSet">Commonly used</option>
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331 <option value="full">Full parameter list</option>
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332 </param>
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333 <when value="preSet" />
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334 <when value="full">
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335 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
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336 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
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337 <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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338 <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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339 <conditional name="alignModeOption">
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340 <param name="alignMode" type="select" label="Alignment mode">
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341 <option value="nMode" selected="true">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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342 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
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343 </param>
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344 <when value="nMode">
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345 <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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346 <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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347 <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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parents:
diff changeset
348 <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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parents:
diff changeset
349 <option value="round">Round to nearest 10</option>
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parents:
diff changeset
350 <option value="noRound">Do not round to nearest 10</option>
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parents:
diff changeset
351 </param>
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parents:
diff changeset
352 </when>
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parents:
diff changeset
353 <when value="vMode">
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parents:
diff changeset
354 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
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parents:
diff changeset
355 </when>
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parents:
diff changeset
356 </conditional>
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parents:
diff changeset
357 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
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parents:
diff changeset
358 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
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parents:
diff changeset
359 <option value="forward">Align against the forward reference strand</option>
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parents:
diff changeset
360 <option value="noForward">Do not align against the forward reference strand</option>
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parents:
diff changeset
361 </param>
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parents:
diff changeset
362 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
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parents:
diff changeset
363 <option value="reverse">Align against the reverse-complement reference strand</option>
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parents:
diff changeset
364 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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parents:
diff changeset
365 </param>
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parents:
diff changeset
366 <conditional name="pBestOption">
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parents:
diff changeset
367 <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">
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parents:
diff changeset
368 <option value="noBest">Do not use best</option>
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parents:
diff changeset
369 <option value="doBest">Use best</option>
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parents:
diff changeset
370 </param>
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parents:
diff changeset
371 <when value="noBest">
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parents:
diff changeset
372 <conditional name="pTryHardOption">
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parents:
diff changeset
373 <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
374 <option value="noTryHard">Do not try hard</option>
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parents:
diff changeset
375 <option value="doTryHard">Try hard</option>
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parents:
diff changeset
376 </param>
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parents:
diff changeset
377 <when value="noTryHard">
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parents:
diff changeset
378 <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)" />
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parents:
diff changeset
379 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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parents:
diff changeset
380 </when>
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parents:
diff changeset
381 <when value="doTryHard" />
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parents:
diff changeset
382 </conditional>
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parents:
diff changeset
383 </when>
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parents:
diff changeset
384 <when value="doBest">
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parents:
diff changeset
385 <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)">
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parents:
diff changeset
386 <option value="noStrata">Do not use strata option</option>
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parents:
diff changeset
387 <option value="doStrata">Use strata option</option>
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parents:
diff changeset
388 </param>
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parents:
diff changeset
389 <conditional name="pTryHardOption">
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parents:
diff changeset
390 <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
391 <option value="noTryHard">Do not try hard</option>
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parents:
diff changeset
392 <option value="doTryHard">Try hard</option>
7e3bd576aa7c Uploaded
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parents:
diff changeset
393 </param>
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parents:
diff changeset
394 <when value="noTryHard">
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parents:
diff changeset
395 <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)" />
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parents:
diff changeset
396 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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parents:
diff changeset
397 </when>
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parents:
diff changeset
398 <when value="doTryHard" />
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parents:
diff changeset
399 </conditional>
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parents:
diff changeset
400 </when>
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parents:
diff changeset
401 </conditional>
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parents:
diff changeset
402 <conditional name="pAllValAlignsOption">
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parents:
diff changeset
403 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
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parents:
diff changeset
404 <option value="noAllValAligns">Do not report all valid alignments</option>
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parents:
diff changeset
405 <option value="doAllValAligns">Report all valid alignments</option>
7e3bd576aa7c Uploaded
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parents:
diff changeset
406 </param>
7e3bd576aa7c Uploaded
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parents:
diff changeset
407 <when value="noAllValAligns">
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parents:
diff changeset
408 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
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parents:
diff changeset
409 </when>
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parents:
diff changeset
410 <when value="doAllValAligns" />
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parents:
diff changeset
411 </conditional>
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parents:
diff changeset
412 <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" />
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parents:
diff changeset
413 <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)" />
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parents:
diff changeset
414 <param name="pUnmappedFile" 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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parents:
diff changeset
415 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
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parents:
diff changeset
416 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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parents:
diff changeset
417 </when> <!-- full -->
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parents:
diff changeset
418 </conditional> <!-- pParams -->
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parents:
diff changeset
419 </when> <!-- paired -->
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parents:
diff changeset
420 </conditional> <!-- singlePaired -->
7e3bd576aa7c Uploaded
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parents:
diff changeset
421 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
422 <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" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
423 </inputs>
7e3bd576aa7c Uploaded
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parents:
diff changeset
424 <outputs>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
425 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
7e3bd576aa7c Uploaded
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parents:
diff changeset
426 <actions>
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parents:
diff changeset
427 <conditional name="refGenomeSource.genomeSource">
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parents:
diff changeset
428 <when value="indexed">
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parents:
diff changeset
429 <action type="metadata" name="dbkey">
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parents:
diff changeset
430 <option type="from_data_table" name="bowtie_genome_indexes" column="1" offset="0">
7e3bd576aa7c Uploaded
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parents:
diff changeset
431 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
7e3bd576aa7c Uploaded
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parents:
diff changeset
432 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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parents:
diff changeset
433 </option>
7e3bd576aa7c Uploaded
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parents:
diff changeset
434 </action>
7e3bd576aa7c Uploaded
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parents:
diff changeset
435 </when>
7e3bd576aa7c Uploaded
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parents:
diff changeset
436 <when value="history">
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parents:
diff changeset
437 <action type="metadata" name="dbkey">
7e3bd576aa7c Uploaded
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parents:
diff changeset
438 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
439 </action>
7e3bd576aa7c Uploaded
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parents:
diff changeset
440 </when>
7e3bd576aa7c Uploaded
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parents:
diff changeset
441 </conditional>
7e3bd576aa7c Uploaded
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parents:
diff changeset
442 </actions>
7e3bd576aa7c Uploaded
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parents:
diff changeset
443 </data>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
444 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
445 <filter>save_mapping_stats is True</filter>
7e3bd576aa7c Uploaded
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parents:
diff changeset
446 </data>
7e3bd576aa7c Uploaded
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parents:
diff changeset
447 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
7e3bd576aa7c Uploaded
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parents:
diff changeset
448 <filter>((
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
449 singlePaired['sPaired'] == "single" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
450 singlePaired['sParams']['sSettingsType'] == "full" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
451 singlePaired['sParams']['sMaxFile'] is True
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
452 ) or (
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
453 singlePaired['sPaired'] == "paired" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
454 singlePaired['pParams']['pSettingsType'] == "full" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
455 singlePaired['pParams']['pMaxFile'] is True
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
456 ))
7e3bd576aa7c Uploaded
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parents:
diff changeset
457 </filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
458 <actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
459 <conditional name="singlePaired.sPaired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
460 <when value="single">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
461 <action type="format">
7e3bd576aa7c Uploaded
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parents:
diff changeset
462 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
463 </action>
7e3bd576aa7c Uploaded
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parents:
diff changeset
464 </when>
7e3bd576aa7c Uploaded
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parents:
diff changeset
465 <when value="paired">
7e3bd576aa7c Uploaded
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parents:
diff changeset
466 <action type="format">
7e3bd576aa7c Uploaded
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parents:
diff changeset
467 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
468 </action>
7e3bd576aa7c Uploaded
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parents:
diff changeset
469 </when>
7e3bd576aa7c Uploaded
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parents:
diff changeset
470 </conditional>
7e3bd576aa7c Uploaded
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parents:
diff changeset
471 </actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
472 </data>
7e3bd576aa7c Uploaded
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parents:
diff changeset
473 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
474 <filter>singlePaired['sPaired'] == "paired"</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
475 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
476 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
477 <actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
478 <conditional name="singlePaired.sPaired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
479 <when value="single">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
480 <action type="format">
7e3bd576aa7c Uploaded
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parents:
diff changeset
481 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
482 </action>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
483 </when>
7e3bd576aa7c Uploaded
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parents:
diff changeset
484 <when value="paired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
485 <action type="format">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
486 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
487 </action>
7e3bd576aa7c Uploaded
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parents:
diff changeset
488 </when>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
489 </conditional>
7e3bd576aa7c Uploaded
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parents:
diff changeset
490 </actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
491 </data>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
492 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
493 <filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
494 ((
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
495 singlePaired['sPaired'] == "single" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
496 singlePaired['sParams']['sSettingsType'] == "full" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
497 singlePaired['sParams']['sUnmappedFile'] is True
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
498 ) or (
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
499 singlePaired['sPaired'] == "paired" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
500 singlePaired['pParams']['pSettingsType'] == "full" and
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
501 singlePaired['pParams']['pUnmappedFile'] is True
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
502 ))
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
503 </filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
504 <actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
505 <conditional name="singlePaired.sPaired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
506 <when value="single">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
507 <action type="format">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
508 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
509 </action>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
510 </when>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
511 <when value="paired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
512 <action type="format">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
513 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
514 </action>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
515 </when>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
516 </conditional>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
517 </actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
518 </data>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
519 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
520 <filter>singlePaired['sPaired'] == "paired"</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
521 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
522 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
523 <actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
524 <conditional name="singlePaired.sPaired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
525 <when value="single">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
526 <action type="format">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
527 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
528 </action>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
529 </when>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
530 <when value="paired">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
531 <action type="format">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
532 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
533 </action>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
534 </when>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
535 </conditional>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
536 </actions>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
537 </data>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
538 </outputs>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
539 <tests>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
540 <test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
541 <!--
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
542 Bowtie command:
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
543 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
544 sort bowtie_out6_u.sam > bowtie_out6.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
545 -p is the number of threads. You need to replace the + with 2 dashes.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
546 chrM_base needs to be the base location/name of the index files.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
547 -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
548 <param name="genomeSource" value="indexed" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
549 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
550 <param name="index" value="equCab2chrM" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
551 <param name="sPaired" value="single" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
552 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
553 <param name="sSettingsType" value="preSet" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
554 <param name="suppressHeader" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
555 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
556 <metadata name="dbkey" value="equCab2" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
557 </output>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
558 </test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
559 <test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
560 <!--
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
561 Bowtie command:
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
562 bowtie-build -f test-data/phiX.fasta phiX_base
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
563 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
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
564 sort bowtie_out7_u.sam > bowtie_out7.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
565 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
566 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
567 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
568 -p is the number of threads. You need to replace the + with 2 dashes.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
569 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
570 chrM_base is the index files' location/base name.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
571 -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
572 <param name="genomeSource" value="history" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
573 <param name="ownFile" value="phiX.fasta" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
574 <param name="indexSettings" value="indexPreSet" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
575 <param name="sPaired" value="paired" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
576 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
577 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
578 <param name="pMaxInsert" value="1000" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
579 <param name="pMateOrient" value="ff" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
580 <param name="pSettingsType" value="full" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
581 <param name="pSkip" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
582 <param name="pAlignLimit" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
583 <param name="pTrimH" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
584 <param name="pTrimL" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
585 <param name="alignMode" value="nMode" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
586 <param name="pMismatchSeed" value="2" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
587 <param name="pMismatchQual" value="70" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
588 <param name="pSeedLen" value="28" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
589 <param name="pRounding" value="round" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
590 <param name="pMinInsert" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
591 <param name="pMaxAlignAttempt" value="100" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
592 <param name="pForwardAlign" value="forward" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
593 <param name="pReverseAlign" value="reverse" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
594 <param name="pTryHard" value="noTryHard" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
595 <param name="pValAlign" value="1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
596 <param name="pAllValAligns" value="noAllValAligns" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
597 <param name="pSuppressAlign" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
598 <param name="pUnmappedFile" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
599 <param name="pMaxFile" value="false" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
600 <param name="pBest" value="doBest" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
601 <param name="pdMaxBacktracks" value="800" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
602 <param name="pdStrata" value="noStrata" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
603 <param name="pOffrate" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
604 <param name="pSeed" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
605 <param name="suppressHeader" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
606 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
607 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
608 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
609 </test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
610 <!-- start testing of non-sanger variant fastq reads -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
611 <test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
612 <param name="genomeSource" value="history" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
613 <param name="ownFile" value="phiX.fasta" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
614 <param name="indexSettings" value="indexPreSet" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
615 <param name="sPaired" value="paired" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
616 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
617 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
618 <param name="pMaxInsert" value="1000" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
619 <param name="pMateOrient" value="ff" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
620 <param name="pSettingsType" value="full" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
621 <param name="pSkip" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
622 <param name="pAlignLimit" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
623 <param name="pTrimH" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
624 <param name="pTrimL" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
625 <param name="alignMode" value="nMode" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
626 <param name="pMismatchSeed" value="2" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
627 <param name="pMismatchQual" value="70" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
628 <param name="pSeedLen" value="28" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
629 <param name="pRounding" value="round" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
630 <param name="pMinInsert" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
631 <param name="pMaxAlignAttempt" value="100" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
632 <param name="pForwardAlign" value="forward" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
633 <param name="pReverseAlign" value="reverse" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
634 <param name="pTryHard" value="noTryHard" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
635 <param name="pValAlign" value="1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
636 <param name="pAllValAligns" value="noAllValAligns" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
637 <param name="pSuppressAlign" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
638 <param name="pUnmappedFile" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
639 <param name="pMaxFile" value="false" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
640 <param name="pBest" value="doBest" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
641 <param name="pdMaxBacktracks" value="800" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
642 <param name="pdStrata" value="noStrata" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
643 <param name="pOffrate" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
644 <param name="pSeed" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
645 <param name="suppressHeader" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
646 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
647 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
648 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
649 </test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
650 <test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
651 <param name="genomeSource" value="history" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
652 <param name="ownFile" value="phiX.fasta" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
653 <param name="indexSettings" value="indexPreSet" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
654 <param name="sPaired" value="paired" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
655 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
656 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
657 <param name="pMaxInsert" value="1000" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
658 <param name="pMateOrient" value="ff" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
659 <param name="pSettingsType" value="full" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
660 <param name="pSkip" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
661 <param name="pAlignLimit" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
662 <param name="pTrimH" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
663 <param name="pTrimL" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
664 <param name="alignMode" value="nMode" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
665 <param name="pMismatchSeed" value="2" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
666 <param name="pMismatchQual" value="70" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
667 <param name="pSeedLen" value="28" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
668 <param name="pRounding" value="round" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
669 <param name="pMinInsert" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
670 <param name="pMaxAlignAttempt" value="100" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
671 <param name="pForwardAlign" value="forward" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
672 <param name="pReverseAlign" value="reverse" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
673 <param name="pTryHard" value="noTryHard" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
674 <param name="pValAlign" value="1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
675 <param name="pAllValAligns" value="noAllValAligns" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
676 <param name="pSuppressAlign" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
677 <param name="pUnmappedFile" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
678 <param name="pMaxFile" value="false" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
679 <param name="pBest" value="doBest" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
680 <param name="pdMaxBacktracks" value="800" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
681 <param name="pdStrata" value="noStrata" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
682 <param name="pOffrate" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
683 <param name="pSeed" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
684 <param name="suppressHeader" value="true" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
685 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
686 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
687 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
688 </test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
689 <!-- end testing of non-sanger variant fastq reads -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
690 <test>
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
691 <!--
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
692 Bowtie command:
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
693 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
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
694 sort bowtie_out9_u.sam > bowtie_out9.sam
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
695 -p is the number of threads. You need to replace the + with 2 dashes.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
696 chrM_base is the index files' location/base name.
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
697 -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
698 <param name="genomeSource" value="indexed" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
699 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
700 <param name="index" value="equCab2chrM" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
701 <param name="sPaired" value="single" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
702 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
703 <param name="sSettingsType" value="full" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
704 <param name="sSkip" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
705 <param name="sAlignLimit" value="-1" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
706 <param name="sTrimH" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
707 <param name="sTrimL" value="0" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
708 <param name="alignMode" value="nMode" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
709 <param name="sMismatchSeed" value="2" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
710 <param name="sMismatchQual" value="70" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
711 <param name="sSeedLen" value="28" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
712 <param name="sRounding" value="round" />
7e3bd576aa7c Uploaded
triasteran
parents:
diff changeset
713 <param name="sForwardAlign" value="forward" />
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parents:
diff changeset
714 <param name="sReverseAlign" value="reverse" />
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parents:
diff changeset
715 <param name="sTryHard" value="doTryHard" />
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parents:
diff changeset
716 <param name="sValAlign" value="1" />
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parents:
diff changeset
717 <param name="sAllValAligns" value="noAllValAligns" />
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parents:
diff changeset
718 <param name="sSuppressAlign" value="-1" />
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parents:
diff changeset
719 <param name="sUnmappedFile" value="false" />
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parents:
diff changeset
720 <param name="sMaxFile" value="false" />
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parents:
diff changeset
721 <param name="sBest" value="noBest" />
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parents:
diff changeset
722 <param name="sOffrate" value="-1" />
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parents:
diff changeset
723 <param name="sSeed" value="-1" />
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parents:
diff changeset
724 <param name="suppressHeader" value="true" />
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parents:
diff changeset
725 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
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parents:
diff changeset
726 <metadata name="dbkey" value="equCab2" />
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parents:
diff changeset
727 </output>
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parents:
diff changeset
728 </test>
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parents:
diff changeset
729 <test>
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parents:
diff changeset
730 <!--
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parents:
diff changeset
731 Bowtie command:
7e3bd576aa7c Uploaded
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parents:
diff changeset
732 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
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parents:
diff changeset
733 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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parents:
diff changeset
734 sort bowtie_out10_u.sam > bowtie_out10.sam
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parents:
diff changeset
735 -p is the number of threads. You need to replace the + with 2 dashes.
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parents:
diff changeset
736 chrM_base is the index files' location/base name.
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parents:
diff changeset
737 -->
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parents:
diff changeset
738 <param name="genomeSource" value="history" />
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parents:
diff changeset
739 <param name="ownFile" value="phiX.fasta" />
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parents:
diff changeset
740 <param name="indexSettings" value="indexFull" />
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parents:
diff changeset
741 <param name="autoB" value="auto" />
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parents:
diff changeset
742 <param name="nodc" value="dc" />
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parents:
diff changeset
743 <param name="noref" value="ref" />
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parents:
diff changeset
744 <param name="offrate" value="5" />
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parents:
diff changeset
745 <param name="ftab" value="10" />
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parents:
diff changeset
746 <param name="ntoa" value="no" />
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parents:
diff changeset
747 <param name="endian" value="little" />
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parents:
diff changeset
748 <param name="seed" value="-1" />
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parents:
diff changeset
749 <param name="sPaired" value="paired" />
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parents:
diff changeset
750 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
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parents:
diff changeset
751 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
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parents:
diff changeset
752 <param name="pMaxInsert" value="1000" />
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parents:
diff changeset
753 <param name="pMateOrient" value="ff" />
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parents:
diff changeset
754 <param name="pSettingsType" value="preSet" />
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parents:
diff changeset
755 <param name="suppressHeader" value="true" />
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parents:
diff changeset
756 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
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parents:
diff changeset
757 </test>
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parents:
diff changeset
758 <test>
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parents:
diff changeset
759 <!--
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parents:
diff changeset
760 Bowtie command:
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parents:
diff changeset
761 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
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parents:
diff changeset
762 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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parents:
diff changeset
763 sort bowtie_out10_u.sam > bowtie_out10.sam
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parents:
diff changeset
764 -p is the number of threads. You need to replace the + with 2 dashes.
7e3bd576aa7c Uploaded
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parents:
diff changeset
765 chrM_base is the index files' location/base name.
7e3bd576aa7c Uploaded
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parents:
diff changeset
766 -->
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parents:
diff changeset
767 <param name="genomeSource" value="history" />
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parents:
diff changeset
768 <param name="ownFile" value="phiX.fasta" />
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parents:
diff changeset
769 <param name="indexSettings" value="indexFull" />
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parents:
diff changeset
770 <param name="autoB" value="auto" />
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parents:
diff changeset
771 <param name="nodc" value="dc" />
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parents:
diff changeset
772 <param name="noref" value="ref" />
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parents:
diff changeset
773 <param name="offrate" value="5" />
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parents:
diff changeset
774 <param name="ftab" value="10" />
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parents:
diff changeset
775 <param name="ntoa" value="no" />
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parents:
diff changeset
776 <param name="endian" value="little" />
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parents:
diff changeset
777 <param name="seed" value="-1" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
778 <param name="sPaired" value="paired" />
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parents:
diff changeset
779 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
7e3bd576aa7c Uploaded
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parents:
diff changeset
780 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
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parents:
diff changeset
781 <param name="pMaxInsert" value="1000" />
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parents:
diff changeset
782 <param name="pMateOrient" value="ff" />
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parents:
diff changeset
783 <param name="pSettingsType" value="preSet" />
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parents:
diff changeset
784 <param name="suppressHeader" value="true" />
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parents:
diff changeset
785 <param name="save_mapping_stats" value="true" />
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parents:
diff changeset
786 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
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parents:
diff changeset
787 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
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parents:
diff changeset
788 </test>
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parents:
diff changeset
789 </tests>
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parents:
diff changeset
790
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parents:
diff changeset
791 <help>
7e3bd576aa7c Uploaded
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parents:
diff changeset
792
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parents:
diff changeset
793 **What it does**
7e3bd576aa7c Uploaded
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parents:
diff changeset
794
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parents:
diff changeset
795 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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parents:
diff changeset
796
7e3bd576aa7c Uploaded
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parents:
diff changeset
797 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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parents:
diff changeset
798
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parents:
diff changeset
799 ------
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parents:
diff changeset
800
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parents:
diff changeset
801 **Know what you are doing**
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parents:
diff changeset
802
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parents:
diff changeset
803 .. class:: warningmark
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parents:
diff changeset
804
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parents:
diff changeset
805 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.
7e3bd576aa7c Uploaded
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parents:
diff changeset
806
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parents:
diff changeset
807 .. __: http://bowtie-bio.sourceforge.net/index.shtml
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parents:
diff changeset
808
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parents:
diff changeset
809 ------
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parents:
diff changeset
810
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parents:
diff changeset
811 **Input formats**
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parents:
diff changeset
812
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parents:
diff changeset
813 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
7e3bd576aa7c Uploaded
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parents:
diff changeset
814
7e3bd576aa7c Uploaded
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parents:
diff changeset
815 ------
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parents:
diff changeset
816
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parents:
diff changeset
817 **A Note on Built-in Reference Genomes**
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parents:
diff changeset
818
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parents:
diff changeset
819 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.
7e3bd576aa7c Uploaded
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parents:
diff changeset
820
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parents:
diff changeset
821 ------
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parents:
diff changeset
822
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parents:
diff changeset
823 **Outputs**
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parents:
diff changeset
824
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parents:
diff changeset
825 The output is in SAM format, and has the following columns::
7e3bd576aa7c Uploaded
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parents:
diff changeset
826
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parents:
diff changeset
827 Column Description
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parents:
diff changeset
828 -------- --------------------------------------------------------
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parents:
diff changeset
829 1 QNAME Query (pair) NAME
7e3bd576aa7c Uploaded
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parents:
diff changeset
830 2 FLAG bitwise FLAG
7e3bd576aa7c Uploaded
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parents:
diff changeset
831 3 RNAME Reference sequence NAME
7e3bd576aa7c Uploaded
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parents:
diff changeset
832 4 POS 1-based leftmost POSition/coordinate of clipped sequence
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parents:
diff changeset
833 5 MAPQ MAPping Quality (Phred-scaled)
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parents:
diff changeset
834 6 CIGAR extended CIGAR string
7e3bd576aa7c Uploaded
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parents:
diff changeset
835 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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parents:
diff changeset
836 8 MPOS 1-based Mate POSition
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parents:
diff changeset
837 9 ISIZE Inferred insert SIZE
7e3bd576aa7c Uploaded
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parents:
diff changeset
838 10 SEQ query SEQuence on the same strand as the reference
7e3bd576aa7c Uploaded
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parents:
diff changeset
839 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
7e3bd576aa7c Uploaded
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parents:
diff changeset
840 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
7e3bd576aa7c Uploaded
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parents:
diff changeset
841
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parents:
diff changeset
842 The flags are as follows::
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parents:
diff changeset
843
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parents:
diff changeset
844 Flag Description
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parents:
diff changeset
845 ------ -------------------------------------
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parents:
diff changeset
846 0x0001 the read is paired in sequencing
7e3bd576aa7c Uploaded
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parents:
diff changeset
847 0x0002 the read is mapped in a proper pair
7e3bd576aa7c Uploaded
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parents:
diff changeset
848 0x0004 the query sequence itself is unmapped
7e3bd576aa7c Uploaded
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parents:
diff changeset
849 0x0008 the mate is unmapped
7e3bd576aa7c Uploaded
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parents:
diff changeset
850 0x0010 strand of the query (1 for reverse)
7e3bd576aa7c Uploaded
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parents:
diff changeset
851 0x0020 strand of the mate
7e3bd576aa7c Uploaded
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parents:
diff changeset
852 0x0040 the read is the first read in a pair
7e3bd576aa7c Uploaded
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parents:
diff changeset
853 0x0080 the read is the second read in a pair
7e3bd576aa7c Uploaded
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parents:
diff changeset
854 0x0100 the alignment is not primary
7e3bd576aa7c Uploaded
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parents:
diff changeset
855
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parents:
diff changeset
856 It looks like this (scroll sideways to see the entire example)::
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parents:
diff changeset
857
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parents:
diff changeset
858 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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parents:
diff changeset
859 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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parents:
diff changeset
860 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
7e3bd576aa7c Uploaded
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parents:
diff changeset
861
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parents:
diff changeset
862 -------
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parents:
diff changeset
863
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parents:
diff changeset
864 **Bowtie settings**
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parents:
diff changeset
865
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parents:
diff changeset
866 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
7e3bd576aa7c Uploaded
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parents:
diff changeset
867
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parents:
diff changeset
868 ------
7e3bd576aa7c Uploaded
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parents:
diff changeset
869
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parents:
diff changeset
870 **Bowtie parameter list**
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parents:
diff changeset
871
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parents:
diff changeset
872 This is an exhaustive list of Bowtie options:
7e3bd576aa7c Uploaded
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parents:
diff changeset
873
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parents:
diff changeset
874 For indexing (bowtie-build)::
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parents:
diff changeset
875
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parents:
diff changeset
876 -a No auto behavior. Disable the default behavior where bowtie automatically
7e3bd576aa7c Uploaded
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parents:
diff changeset
877 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
7e3bd576aa7c Uploaded
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parents:
diff changeset
878 to the memory available. [off]
7e3bd576aa7c Uploaded
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parents:
diff changeset
879 --packed Packing. Use a packed representation for DNA strings. [auto]
7e3bd576aa7c Uploaded
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parents:
diff changeset
880 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
7e3bd576aa7c Uploaded
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parents:
diff changeset
881 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
7e3bd576aa7c Uploaded
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parents:
diff changeset
882 expressed as a fraction of the length of the reference. [4]
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parents:
diff changeset
883 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
7e3bd576aa7c Uploaded
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parents:
diff changeset
884 sample. [1024]
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parents:
diff changeset
885 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
7e3bd576aa7c Uploaded
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parents:
diff changeset
886 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
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parents:
diff changeset
887 of the index. Used only for paired-end alignment. [off]
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parents:
diff changeset
888 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
7e3bd576aa7c Uploaded
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parents:
diff changeset
889 indexer will mark every 2^INT rows. The marked rows correspond to rows on
7e3bd576aa7c Uploaded
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parents:
diff changeset
890 the genome. [5]
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parents:
diff changeset
891 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
7e3bd576aa7c Uploaded
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parents:
diff changeset
892 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
7e3bd576aa7c Uploaded
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parents:
diff changeset
893 bytes. [10]
7e3bd576aa7c Uploaded
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parents:
diff changeset
894 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
7e3bd576aa7c Uploaded
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parents:
diff changeset
895 simply excluded from the index and Bowtie will not find alignments that
7e3bd576aa7c Uploaded
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parents:
diff changeset
896 overlap them. [off]
7e3bd576aa7c Uploaded
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parents:
diff changeset
897 --big Endianness. Endianness to use when serializing integers to the index file. [off]
7e3bd576aa7c Uploaded
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parents:
diff changeset
898 --little Endianness. [--little]
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parents:
diff changeset
899 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
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parents:
diff changeset
900
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parents:
diff changeset
901 For aligning (bowtie)::
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parents:
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902
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parents:
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903 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
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parents:
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904 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
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parents:
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905 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
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parents:
diff changeset
906 read before alignment. [0]
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parents:
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907 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
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parents:
diff changeset
908 read before alignment. [0]
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parents:
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909 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
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parents:
diff changeset
910 with seed length option). Can be 0, 1, 2, or 3. [2]
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parents:
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911 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
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912 read positions. Bowtie rounds quality values to the nearest 10 and saturates
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parents:
diff changeset
913 at 30. [70]
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parents:
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914 -l INT Seed length. The number of bases on the high-quality end of the read to
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parents:
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915 which the -n ceiling applies. Must be at least 5. [28]
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parents:
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916 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
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parents:
diff changeset
917 saturate at 30. This options turns off that rounding. [off]
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parents:
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918 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
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parents:
diff changeset
919 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
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parents:
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920 with at most INT mismatches. [off]
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parents:
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921 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
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parents:
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922 Does checking on untrimmed reads if -5 or -3 is used. [0]
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parents:
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923 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
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parents:
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924 Does checking on untrimmed reads if -5 or -3 is used. [250]
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parents:
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925 --fr Mate orientation. The upstream/downstream mate orientations for a valid
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parents:
diff changeset
926 paired-end alignment against the forward reference strand. [--fr]
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parents:
diff changeset
927 --rf Mate orientation. [off]
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parents:
diff changeset
928 --ff Mate orientation. [off]
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parents:
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929 --pairtries INT Maximum alignment attempts for paired-end data. [100]
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parents:
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930 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
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parents:
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931 to align against the forward reference strand. [off]
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parents:
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932 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
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parents:
diff changeset
933 attempt to align against the reverse-complement reference strand. [off]
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parents:
diff changeset
934 --un FILENAME Write all reads that could not be aligned to file [off]
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parents:
diff changeset
935 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
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parents:
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936 set with the -m option to file [off]
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parents:
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937 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
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parents:
diff changeset
938 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
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939 -y Try hard. Try as hard as possible to find valid alignments when they exist,
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parents:
diff changeset
940 including paired-end alignments. [off]
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parents:
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941 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
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triasteran
parents:
diff changeset
942 store path descriptors in --best mode. [32]
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parents:
diff changeset
943 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
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parents:
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944 -a All valid alignments. Choosing this means that all valid alignments per read
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parents:
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945 or pair will be reported. [off]
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parents:
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946 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
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parents:
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947 if more than INT reportable alignments exist for it. [no limit]
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parents:
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948 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
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parents:
diff changeset
949 "best" in terms of stratum (the number of mismatches) and quality values at
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parents:
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950 mismatched position. [off]
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parents:
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951 --strata Best strata. When running in best mode, report alignments that fall into the
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parents:
diff changeset
952 best stratum if there are ones falling into more than one. [off]
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parents:
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953 -o INT Offrate override. Override the offrate of the index with INT. Some row
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parents:
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954 markings are discarded when index read into memory. INT must be greater than
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parents:
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955 the value used to build the index (default: 5). [off]
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parents:
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956 --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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957 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
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parents:
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958 SNPs per base in the subject genome. [see --snpfrac]
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parents:
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959 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
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parents:
diff changeset
960 alignments. [0.001]
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parents:
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961 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
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parents:
diff changeset
962 alignments. [off]
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parents:
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963
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parents:
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964 </help>
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parents:
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965 <citations>
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parents:
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966 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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parents:
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967 </citations>
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968 </tool>