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1 <tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="0.1.1e">
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2 <requirements>
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3 <requirement type="package" version="1.3.1">bowtie</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 python '$__tool_directory__/bowtie_wrapper_py3_a.py'
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7 ## Set number of threads
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8 --threads="\${GALAXY_SLOTS:-4}"
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9 ## Outputs
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10 --output="${output}"
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11 #if str( $singlePaired.sPaired ) == "single"
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12 #if $output_unmapped_reads_l
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13 --output_unmapped_reads="${output_unmapped_reads_l}"
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14 #end if
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15 #if $output_suppressed_reads_l
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16 --output_suppressed_reads="${output_suppressed_reads_l}"
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17 #end if
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18 --galaxy_input_format="${singlePaired.sInput1.ext}"
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19 #else
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20 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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21 --output_unmapped_reads_l="${output_unmapped_reads_l}"
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22 --output_unmapped_reads_r="${output_unmapped_reads_r}"
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23 #end if
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24 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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25 --output_suppressed_reads_l="${output_suppressed_reads_l}"
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26 --output_suppressed_reads_r="${output_suppressed_reads_r}"
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27 #end if
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28 --galaxy_input_format="${singlePaired.pInput1.ext}"
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29 #end if
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30 ## Inputs
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31 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
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32 --suppressHeader="${suppressHeader}"
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33 --genomeSource="${refGenomeSource.genomeSource}"
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34 #if $refGenomeSource.genomeSource == "history":
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35 ##index already exists
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36 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
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37 ##user previously built
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38 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
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39 --do_not_build_index
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40 #else:
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41 ##build index on the fly
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42 --ref="${refGenomeSource.ownFile}"
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43 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
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44 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
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45 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
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46 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
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47 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
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48 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
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49 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
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50 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
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51 #end if
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52 --inodc="${refGenomeSource.indexParams.nodc}"
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53 --inoref="${refGenomeSource.indexParams.noref}"
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54 --ioffrate="${refGenomeSource.indexParams.offrate}"
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55 --iftab="${refGenomeSource.indexParams.ftab}"
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56 --intoa="${refGenomeSource.indexParams.ntoa}"
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57 --iendian="${refGenomeSource.indexParams.endian}"
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58 --iseed="${refGenomeSource.indexParams.seed}"
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59 --icutoff="${refGenomeSource.indexParams.cutoff}"
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60 #end if
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61 #end if
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62 #else
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63 ##use pre-built index
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64 --ref="${refGenomeSource.index.fields.path}"
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65 #end if
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66 --paired="${singlePaired.sPaired}"
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67 #if $singlePaired.sPaired == "single":
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68 --input1="${singlePaired.sInput1}"
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69 --params="${singlePaired.sParams.sSettingsType}"
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70 #if $singlePaired.sParams.sSettingsType == "full":
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71 --skip="${singlePaired.sParams.sSkip}"
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72 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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73 --trimH="${singlePaired.sParams.sTrimH}"
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74 --trimL="${singlePaired.sParams.sTrimL}"
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75 --mismatchSeed="${singlePaired.sParams.sMismatchSeed}"
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76 --mismatchQual="${singlePaired.sParams.sMismatchQual}"
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77 --seedLen="${singlePaired.sParams.sSeedLen}"
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78 --rounding="${singlePaired.sParams.sRounding}"
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79 --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}"
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80 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
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81 --tryHard="${singlePaired.sParams.sTryHard}"
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82 --valAlign="${singlePaired.sParams.sValAlign}"
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83 --allValAligns="${singlePaired.sParams.sAllValAligns}"
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84 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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85 --best="${singlePaired.sParams.sBestOption.sBest}"
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86 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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87 --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}"
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88 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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89 #else:
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90 --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}"
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91 #end if
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92 --offrate="${singlePaired.sParams.sOffrate}"
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93 --seed="${singlePaired.sParams.sSeed}"
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94 #end if
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95 #else:
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96 --input1="${singlePaired.pInput1}"
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97 --input2="${singlePaired.pInput2}"
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98 --maxInsert="${singlePaired.pMaxInsert}"
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99 --mateOrient="${singlePaired.pMateOrient}"
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100 --params="${singlePaired.pParams.pSettingsType}"
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101 #if $singlePaired.pParams.pSettingsType == "full":
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102 --skip="${singlePaired.pParams.pSkip}"
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103 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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104 --trimH="${singlePaired.pParams.pTrimH}"
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105 --trimL="${singlePaired.pParams.pTrimL}"
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106 --mismatchSeed="${singlePaired.pParams.pMismatchSeed}"
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107 --mismatchQual="${singlePaired.pParams.pMismatchQual}"
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108 --seedLen="${singlePaired.pParams.pSeedLen}"
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109 --rounding="${singlePaired.pParams.pRounding}"
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110 --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}"
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111 --minInsert="${singlePaired.pParams.pMinInsert}"
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112 --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}"
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113 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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114 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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115 --tryHard="${singlePaired.pParams.pTryHard}"
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116 --valAlign="${singlePaired.pParams.pValAlign}"
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117 --allValAligns="${singlePaired.pParams.pAllValAligns}"
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118 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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119 --best="${singlePaired.pParams.pBestOption.pBest}"
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120 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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121 --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}"
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122 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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123 #else:
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124 --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}"
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125 #end if
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126 --offrate="${singlePaired.pParams.pOffrate}"
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127 --seed="${singlePaired.pParams.pSeed}"
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128 #end if
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129 #end if
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130 ]]></command>
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131 <inputs>
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132 <conditional name="refGenomeSource">
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133 <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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134 <option value="indexed">Use a built-in index</option>
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135 <option value="history">Use one from the history</option>
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136 </param>
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137 <when value="indexed">
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138 <param name="index" type="select" label="Select the appropriate rRNA index" help="If the rRNA index for your organism is not listed, you will need to upload a fasta file of the rRNA sequences. ">
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139 <options from_data_table="bowtie_rrna_indexes">
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140 <filter type="sort_by" column="2" />
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141 <validator type="no_options" message="No indexes are available" />
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142 </options>
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143 </param>
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144 </when>
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145 <when value="history">
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146 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
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147 <conditional name="indexParams">
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148 <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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149 <option value="indexPreSet">Default</option>
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150 <option value="indexFull">Set your own</option>
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151 </param>
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152 <when value="indexPreSet" />
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153 <when value="indexFull">
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154 <conditional name="autoBehavior">
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155 <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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156 <option value="auto">Automatic behavior</option>
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157 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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158 </param>
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159 <when value="auto" />
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160 <when value="set">
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161 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
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162 <option value="unpacked">Use regular representation</option>
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163 <option value="packed">Use packed representation</option>
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164 </param>
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165 <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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166 <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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167 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
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168 </when>
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169 </conditional>
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170 <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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171 <option value="dc">Use difference-cover sample</option>
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172 <option value="nodc">Disable difference-cover sample</option>
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173 </param>
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174 <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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175 <option value="ref">Build all index files</option>
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176 <option value="noref">Do not build paired-end alignment index files</option>
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177 </param>
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178 <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
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179 <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" />
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180 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
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181 <option value="no">Do not convert Ns</option>
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182 <option value="yes">Convert Ns to As</option>
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183 </param>
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184 <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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185 <option value="little">Little</option>
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186 <option value="big">Big</option>
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187 </param>
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188 <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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189 <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
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190 </when> <!-- indexFull -->
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191 </conditional> <!-- indexParams -->
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192 </when> <!-- history -->
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193 </conditional> <!-- refGenomeSource -->
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194 <conditional name="singlePaired">
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195 <param name="sPaired" type="select" label="Is this library mate-paired?">
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196 <option value="single">Single-end</option>
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197 <option value="paired">Paired-end</option>
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198 </param>
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199 <when value="single">
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200 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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201 <conditional name="sParams">
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202 <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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203 <option value="preSet">Commonly used</option>
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204 <option value="full" selected="true">Full parameter list</option>
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205 </param>
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206 <when value="preSet" />
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207 <when value="full">
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208 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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209 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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210 <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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211 <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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212 <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
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213 <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
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214 <param name="sSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" />
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215 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
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216 <option value="round">Round to nearest 10</option>
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217 <option value="noRound">Do not round to nearest 10</option>
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218 </param>
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219 <param name="sMaqSoapAlign" type="integer" value="3" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
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220 <param name="sReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
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221 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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222 <option value="reverse">Align against the reverse-complement reference strand</option>
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223 </param>
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224 <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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225 <option value="noTryHard">Do not try hard</option>
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226 <option value="doTryHard">Try hard</option>
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227 </param>
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228 <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
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229 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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230 <option value="noAllValAligns">Do not report all valid alignments</option>
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231 <option value="doAllValAligns">Report all valid alignments</option>
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232 </param>
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233 <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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234 <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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235 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" />
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236 <conditional name="sBestOption">
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237 <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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238 <option value="noBest">Do not use best</option>
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239 <option value="doBest">Use best</option>
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240 </param>
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241 <when value="noBest">
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242 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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243 </when>
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244 <when value="doBest">
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245 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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246 <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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247 <option value="noStrata">Do not use strata option</option>
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248 <option value="doStrata">Use strata option</option>
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249 </param>
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250 </when>
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251 </conditional> <!-- bestOption -->
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252 <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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253 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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254 </when> <!-- full -->
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255 </conditional> <!-- sParams -->
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256 </when> <!-- single -->
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257 <when value="paired">
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258 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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259 <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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260 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
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261 <column name="name" index="0"/>
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262 <column name="value" index="0"/>
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263 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
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264 </options>
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265 </param>
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266 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
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267 <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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268 <option value="fr">FR (for Illumina)</option>
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269 <option value="rf">RF</option>
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270 <option value="ff">FF (for SOLiD)</option>
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271 </param>
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272 <conditional name="pParams">
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273 <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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274 <option value="preSet">Commonly used</option>
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275 <option value="full">Full parameter list</option>
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276 </param>
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277 <when value="preSet" />
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278 <when value="full">
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279 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
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280 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
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281 <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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282 <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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283 <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
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284 <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
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285 <param name="pSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" />
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286 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
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287 <option value="round">Round to nearest 10</option>
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288 <option value="noRound">Do not round to nearest 10</option>
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289 </param>
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290 <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
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291 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
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292 <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
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293 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)">
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294 <option value="forward">Align against the forward reference strand</option>
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295 <option value="noForward">Do not align against the forward reference strand</option>
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296 </param>
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297 <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
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298 <option value="reverse">Align against the reverse-complement reference strand</option>
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299 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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300 </param>
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301 <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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302 <option value="noTryHard">Do not try hard</option>
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303 <option value="doTryHard">Try hard</option>
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304 </param>
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305 <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
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306 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
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307 <option value="noAllValAligns">Do not report all valid alignments</option>
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308 <option value="doAllValAligns">Report all valid alignments</option>
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309 </param>
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310 <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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311 <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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312 <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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313 <conditional name="pBestOption">
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314 <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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315 <option value="noBest">Do not use best</option>
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316 <option value="doBest">Use best</option>
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317 </param>
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318 <when value="noBest">
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319 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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320 </when>
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321 <when value="doBest">
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322 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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323 <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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324 <option value="noStrata">Do not use strata option</option>
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325 <option value="doStrata">Use strata option</option>
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326 </param>
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327 </when>
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328 </conditional>
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329 <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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330 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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331 </when> <!-- full -->
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332 </conditional> <!-- pParams -->
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333 </when> <!-- paired -->
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334 </conditional> <!-- singlePaired -->
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335 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
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336 </inputs>
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337 <outputs>
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338 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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339 <actions>
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340 <conditional name="refGenomeSource.genomeSource">
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341 <when value="indexed">
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342 <action type="metadata" name="dbkey">
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343 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
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344 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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345 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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346 </option>
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347 </action>
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348 </when>
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349 <when value="history">
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350 <action type="metadata" name="dbkey">
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351 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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352 </action>
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353 </when>
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354 </conditional>
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355 </actions>
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356 </data>
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357 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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358 <filter>((
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359 singlePaired['sPaired'] == "single" and
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360 singlePaired['sParams']['sSettingsType'] == "full" and
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361 singlePaired['sParams']['sMaxFile'] is True
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|
|
362 ) or (
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363 singlePaired['sPaired'] == "paired" and
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364 singlePaired['pParams']['pSettingsType'] == "full" and
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365 singlePaired['pParams']['pMaxFile'] is True
|
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366 ))
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|
367 </filter>
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368 <actions>
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369 <conditional name="singlePaired.sPaired">
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370 <when value="single">
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371 <action type="format">
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|
372 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
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373 </action>
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374 </when>
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375 <when value="paired">
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376 <action type="format">
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377 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
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378 </action>
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379 </when>
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380 </conditional>
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381 </actions>
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382 </data>
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383 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
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|
384 <filter>singlePaired['sPaired'] == "paired"</filter>
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|
385 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
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|
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386 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
|
|
|
387 <actions>
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|
|
388 <conditional name="singlePaired.sPaired">
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|
|
389 <when value="single">
|
|
|
390 <action type="format">
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|
|
391 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
|
|
|
392 </action>
|
|
|
393 </when>
|
|
|
394 <when value="paired">
|
|
|
395 <action type="format">
|
|
|
396 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
|
|
|
397 </action>
|
|
|
398 </when>
|
|
|
399 </conditional>
|
|
|
400 </actions>
|
|
|
401 </data>
|
|
|
402 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
|
|
|
403 <filter>
|
|
|
404 ((
|
|
|
405 singlePaired['sPaired'] == "single" and
|
|
|
406 singlePaired['sParams']['sSettingsType'] == "full" and
|
|
|
407 singlePaired['sParams']['sUnmappedFile'] is True
|
|
|
408 ) or (
|
|
|
409 singlePaired['sPaired'] == "paired" and
|
|
|
410 singlePaired['pParams']['pSettingsType'] == "full" and
|
|
|
411 singlePaired['pParams']['pUnmappedFile'] is True
|
|
|
412 ))
|
|
|
413 </filter>
|
|
|
414 <actions>
|
|
|
415 <conditional name="singlePaired.sPaired">
|
|
|
416 <when value="single">
|
|
|
417 <action type="format">
|
|
|
418 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
|
|
|
419 </action>
|
|
|
420 </when>
|
|
|
421 <when value="paired">
|
|
|
422 <action type="format">
|
|
|
423 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
|
|
|
424 </action>
|
|
|
425 </when>
|
|
|
426 </conditional>
|
|
|
427 </actions>
|
|
|
428 </data>
|
|
|
429 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
|
|
|
430 <filter>singlePaired['sPaired'] == "paired"</filter>
|
|
|
431 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
|
|
|
432 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
|
|
|
433 <actions>
|
|
|
434 <conditional name="singlePaired.sPaired">
|
|
|
435 <when value="single">
|
|
|
436 <action type="format">
|
|
|
437 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
|
|
|
438 </action>
|
|
|
439 </when>
|
|
|
440 <when value="paired">
|
|
|
441 <action type="format">
|
|
|
442 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
|
|
|
443 </action>
|
|
|
444 </when>
|
|
|
445 </conditional>
|
|
|
446 </actions>
|
|
|
447 </data>
|
|
|
448 </outputs>
|
|
|
449 <tests>
|
|
|
450 <test>
|
|
|
451 <!--
|
|
|
452 Bowtie command:
|
|
|
453 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
|
|
|
454 sort bowtie_out6_u.sam > bowtie_out6.sam
|
|
|
455 -p is the number of threads. You need to replace the + with 2 dashes.
|
|
|
456 chrM_base needs to be the base location/name of the index files.
|
|
|
457 -->
|
|
|
458 <param name="genomeSource" value="indexed" />
|
|
|
459 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
|
|
|
460 <param name="index" value="equCab2chrM" />
|
|
|
461 <param name="sPaired" value="single" />
|
|
|
462 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
|
|
|
463 <param name="sSettingsType" value="preSet" />
|
|
|
464 <param name="suppressHeader" value="true" />
|
|
|
465 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
|
|
|
466 </test>
|
|
|
467 <test>
|
|
|
468 <!--
|
|
|
469 Bowtie command:
|
|
|
470 bowtie-build -f test-data/phiX.fasta phiX_base
|
|
|
471 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
|
|
|
472 sort bowtie_out7_u.sam > bowtie_out7.sam
|
|
|
473 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
|
|
|
474 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
|
|
|
475 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
|
|
|
476 -p is the number of threads. You need to replace the + with 2 dashes.
|
|
|
477 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
|
|
|
478 chrM_base is the index files' location/base name.
|
|
|
479 -->
|
|
|
480 <param name="genomeSource" value="history" />
|
|
|
481 <param name="ownFile" value="phiX.fasta" />
|
|
|
482 <param name="indexSettings" value="indexPreSet" />
|
|
|
483 <param name="sPaired" value="paired" />
|
|
|
484 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
|
|
|
485 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
|
|
|
486 <param name="pMaxInsert" value="1000" />
|
|
|
487 <param name="pMateOrient" value="ff" />
|
|
|
488 <param name="pSettingsType" value="full" />
|
|
|
489 <param name="pSkip" value="0" />
|
|
|
490 <param name="pAlignLimit" value="-1" />
|
|
|
491 <param name="pTrimH" value="0" />
|
|
|
492 <param name="pTrimL" value="0" />
|
|
|
493 <param name="pMismatchSeed" value="2" />
|
|
|
494 <param name="pMismatchQual" value="70" />
|
|
|
495 <param name="pSeedLen" value="25" />
|
|
|
496 <param name="pRounding" value="round" />
|
|
|
497 <param name="pMaqSoapAlign" value="-1" />
|
|
|
498 <param name="pMinInsert" value="0" />
|
|
|
499 <param name="pMaxAlignAttempt" value="100" />
|
|
|
500 <param name="pForwardAlign" value="forward" />
|
|
|
501 <param name="pReverseAlign" value="reverse" />
|
|
|
502 <param name="pTryHard" value="noTryHard" />
|
|
|
503 <param name="pValAlign" value="1" />
|
|
|
504 <param name="pAllValAligns" value="noAllValAligns" />
|
|
|
505 <param name="pSuppressAlign" value="-1" />
|
|
|
506 <param name="pUnmappedFile" value="true" />
|
|
|
507 <param name="pMaxFile" value="false" />
|
|
|
508 <param name="pBest" value="doBest" />
|
|
|
509 <param name="pdMaxBacktracks" value="800" />
|
|
|
510 <param name="pdStrata" value="noStrata" />
|
|
|
511 <param name="pOffrate" value="-1" />
|
|
|
512 <param name="pSeed" value="-1" />
|
|
|
513 <param name="suppressHeader" value="true" />
|
|
|
514 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
|
|
|
515 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
|
|
|
516 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
|
|
|
517 </test>
|
|
|
518 <!-- start testing of non-sanger variant fastq reads -->
|
|
|
519 <test>
|
|
|
520 <param name="genomeSource" value="history" />
|
|
|
521 <param name="ownFile" value="phiX.fasta" />
|
|
|
522 <param name="indexSettings" value="indexPreSet" />
|
|
|
523 <param name="sPaired" value="paired" />
|
|
|
524 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
|
|
|
525 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
|
|
|
526 <param name="pMaxInsert" value="1000" />
|
|
|
527 <param name="pMateOrient" value="ff" />
|
|
|
528 <param name="pSettingsType" value="full" />
|
|
|
529 <param name="pSkip" value="0" />
|
|
|
530 <param name="pAlignLimit" value="-1" />
|
|
|
531 <param name="pTrimH" value="0" />
|
|
|
532 <param name="pTrimL" value="0" />
|
|
|
533 <param name="pMismatchSeed" value="2" />
|
|
|
534 <param name="pMismatchQual" value="70" />
|
|
|
535 <param name="pSeedLen" value="25" />
|
|
|
536 <param name="pRounding" value="round" />
|
|
|
537 <param name="pMaqSoapAlign" value="-1" />
|
|
|
538 <param name="pMinInsert" value="0" />
|
|
|
539 <param name="pMaxAlignAttempt" value="100" />
|
|
|
540 <param name="pForwardAlign" value="forward" />
|
|
|
541 <param name="pReverseAlign" value="reverse" />
|
|
|
542 <param name="pTryHard" value="noTryHard" />
|
|
|
543 <param name="pValAlign" value="1" />
|
|
|
544 <param name="pAllValAligns" value="noAllValAligns" />
|
|
|
545 <param name="pSuppressAlign" value="-1" />
|
|
|
546 <param name="pUnmappedFile" value="true" />
|
|
|
547 <param name="pMaxFile" value="false" />
|
|
|
548 <param name="pBest" value="doBest" />
|
|
|
549 <param name="pdMaxBacktracks" value="800" />
|
|
|
550 <param name="pdStrata" value="noStrata" />
|
|
|
551 <param name="pOffrate" value="-1" />
|
|
|
552 <param name="pSeed" value="-1" />
|
|
|
553 <param name="suppressHeader" value="true" />
|
|
|
554 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
|
|
|
555 <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
|
|
|
556 <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
|
|
|
557 </test>
|
|
|
558 <test>
|
|
|
559 <param name="genomeSource" value="history" />
|
|
|
560 <param name="ownFile" value="phiX.fasta" />
|
|
|
561 <param name="indexSettings" value="indexPreSet" />
|
|
|
562 <param name="sPaired" value="paired" />
|
|
|
563 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
|
|
|
564 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
|
|
|
565 <param name="pMaxInsert" value="1000" />
|
|
|
566 <param name="pMateOrient" value="ff" />
|
|
|
567 <param name="pSettingsType" value="full" />
|
|
|
568 <param name="pSkip" value="0" />
|
|
|
569 <param name="pAlignLimit" value="-1" />
|
|
|
570 <param name="pTrimH" value="0" />
|
|
|
571 <param name="pTrimL" value="0" />
|
|
|
572 <param name="pMismatchSeed" value="2" />
|
|
|
573 <param name="pMismatchQual" value="70" />
|
|
|
574 <param name="pSeedLen" value="25" />
|
|
|
575 <param name="pRounding" value="round" />
|
|
|
576 <param name="pMaqSoapAlign" value="-1" />
|
|
|
577 <param name="pMinInsert" value="0" />
|
|
|
578 <param name="pMaxAlignAttempt" value="100" />
|
|
|
579 <param name="pForwardAlign" value="forward" />
|
|
|
580 <param name="pReverseAlign" value="reverse" />
|
|
|
581 <param name="pTryHard" value="noTryHard" />
|
|
|
582 <param name="pValAlign" value="1" />
|
|
|
583 <param name="pAllValAligns" value="noAllValAligns" />
|
|
|
584 <param name="pSuppressAlign" value="-1" />
|
|
|
585 <param name="pUnmappedFile" value="true" />
|
|
|
586 <param name="pMaxFile" value="false" />
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587 <param name="pBest" value="doBest" />
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588 <param name="pdMaxBacktracks" value="800" />
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589 <param name="pdStrata" value="noStrata" />
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590 <param name="pOffrate" value="-1" />
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591 <param name="pSeed" value="-1" />
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592 <param name="suppressHeader" value="true" />
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593 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
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594 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
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595 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
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596 </test>
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597 <!-- end testing of non-sanger variant fastq reads -->
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598 <test>
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599 <!--
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600 Bowtie command:
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601 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 25 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
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602 sort bowtie_out9_u.sam > bowtie_out9.sam
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603 -p is the number of threads. You need to replace the + with 2 dashes.
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604 chrM_base is the index files' location/base name.
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605 -->
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606 <param name="genomeSource" value="indexed" />
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607 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
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608 <param name="index" value="equCab2chrM" />
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609 <param name="sPaired" value="single" />
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610 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
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611 <param name="sSettingsType" value="full" />
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612 <param name="sSkip" value="0" />
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613 <param name="sAlignLimit" value="-1" />
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614 <param name="sTrimH" value="0" />
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615 <param name="sTrimL" value="0" />
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616 <param name="sMismatchSeed" value="2" />
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617 <param name="sMismatchQual" value="70" />
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618 <param name="sSeedLen" value="25" />
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619 <param name="sRounding" value="round" />
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620 <param name="sMaqSoapAlign" value="-1" />
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621 <param name="sTryHard" value="doTryHard" />
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622 <param name="sValAlign" value="1" />
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623 <param name="sAllValAligns" value="noAllValAligns" />
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624 <param name="sSuppressAlign" value="-1" />
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625 <param name="sUnmappedFile" value="false" />
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626 <param name="sMaxFile" value="false" />
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627 <param name="sBest" value="noBest" />
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628 <param name="snMaxBacktracks" value="125" />
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629 <param name="sOffrate" value="-1" />
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630 <param name="sSeed" value="-1" />
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631 <param name="suppressHeader" value="true" />
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632 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
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633 </test>
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634 <test>
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635 <!--
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|
636 Bowtie command:
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637 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
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|
|
638 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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639 sort bowtie_out10_u.sam > bowtie_out10.sam
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640 -p is the number of threads. You need to replace the + with 2 dashes.
|
|
|
641 chrM_base is the index files' location/base name.
|
|
|
642 -->
|
|
|
643 <param name="genomeSource" value="history" />
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|
|
644 <param name="ownFile" value="phiX.fasta" />
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|
|
645 <param name="indexSettings" value="indexFull" />
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|
|
646 <param name="autoB" value="auto" />
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|
|
647 <param name="nodc" value="dc" />
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|
|
648 <param name="noref" value="ref" />
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|
|
649 <param name="offrate" value="5" />
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|
|
650 <param name="ftab" value="10" />
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|
|
651 <param name="ntoa" value="no" />
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|
|
652 <param name="endian" value="little" />
|
|
|
653 <param name="seed" value="-1" />
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|
|
654 <param name="cutoff" value="-1" />
|
|
|
655 <param name="sPaired" value="paired" />
|
|
|
656 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
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|
|
657 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
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|
|
658 <param name="pMaxInsert" value="1000" />
|
|
|
659 <param name="pMateOrient" value="ff" />
|
|
|
660 <param name="pSettingsType" value="preSet" />
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|
|
661 <param name="suppressHeader" value="true" />
|
|
|
662 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
|
|
|
663 </test>
|
|
|
664 </tests>
|
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|
665 <help>
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|
|
666 <![CDATA[
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|
|
667 Bowtie is a short read aligner.
|
|
|
668 ]]>
|
|
|
669 </help>
|
|
|
670 <citations>
|
|
|
671 <citation type="bibtex">
|
|
|
672 @misc{githubbowtie,
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|
|
673 author = {LastTODO, FirstTODO},
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|
|
674 year = {TODO},
|
|
|
675 title = {bowtie},
|
|
|
676 publisher = {GitHub},
|
|
|
677 journal = {GitHub repository},
|
|
|
678 url = {https://github.com/BenLangmead/bowtie},
|
|
|
679 }</citation>
|
|
|
680 </citations>
|
|
|
681 </tool>
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