annotate bowtie_wrapper.xml @ 1:86d20727b5a9 draft default tip

Added README file
author "Shantanu Pavgi <pavgi@uab.edu>"
date Mon, 26 Aug 2013 16:02:58 -0500
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1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2">
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2 <requirements>
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3 <requirement type='package' version="0.12.7">bowtie</requirement>
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4 </requirements>
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5 <description></description>
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6 <parallelism method="basic"></parallelism>
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7 <command interpreter="python">
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8 bowtie_wrapper.py
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9 ## Hackish setting of number of threads
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10 --threads="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 --icutoff="${refGenomeSource.indexParams.cutoff}"
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62 #end if
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63 #end if
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64 #else
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65 ##use pre-built index
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66 --ref="${refGenomeSource.index.fields.path}"
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67 #end if
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68 --paired="${singlePaired.sPaired}"
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69 #if $singlePaired.sPaired == "single":
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70 --input1="${singlePaired.sInput1}"
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71 --params="${singlePaired.sParams.sSettingsType}"
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72 #if $singlePaired.sParams.sSettingsType == "full":
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73 --skip="${singlePaired.sParams.sSkip}"
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74 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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75 --trimH="${singlePaired.sParams.sTrimH}"
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76 --trimL="${singlePaired.sParams.sTrimL}"
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77 --mismatchSeed="${singlePaired.sParams.sMismatchSeed}"
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78 --mismatchQual="${singlePaired.sParams.sMismatchQual}"
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79 --seedLen="${singlePaired.sParams.sSeedLen}"
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80 --rounding="${singlePaired.sParams.sRounding}"
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81 --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}"
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82 --tryHard="${singlePaired.sParams.sTryHard}"
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83 --valAlign="${singlePaired.sParams.sValAlign}"
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84 --allValAligns="${singlePaired.sParams.sAllValAligns}"
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85 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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86 --best="${singlePaired.sParams.sBestOption.sBest}"
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87 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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88 --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}"
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89 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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90 #else:
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91 --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}"
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92 #end if
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93 --offrate="${singlePaired.sParams.sOffrate}"
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94 --seed="${singlePaired.sParams.sSeed}"
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95 #end if
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96 #else:
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97 --input1="${singlePaired.pInput1}"
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98 --input2="${singlePaired.pInput2}"
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99 --maxInsert="${singlePaired.pMaxInsert}"
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100 --mateOrient="${singlePaired.pMateOrient}"
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101 --params="${singlePaired.pParams.pSettingsType}"
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102 #if $singlePaired.pParams.pSettingsType == "full":
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103 --skip="${singlePaired.pParams.pSkip}"
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104 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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105 --trimH="${singlePaired.pParams.pTrimH}"
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106 --trimL="${singlePaired.pParams.pTrimL}"
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107 --mismatchSeed="${singlePaired.pParams.pMismatchSeed}"
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108 --mismatchQual="${singlePaired.pParams.pMismatchQual}"
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109 --seedLen="${singlePaired.pParams.pSeedLen}"
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110 --rounding="${singlePaired.pParams.pRounding}"
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111 --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}"
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112 --minInsert="${singlePaired.pParams.pMinInsert}"
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113 --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}"
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114 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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115 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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116 --tryHard="${singlePaired.pParams.pTryHard}"
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117 --valAlign="${singlePaired.pParams.pValAlign}"
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118 --allValAligns="${singlePaired.pParams.pAllValAligns}"
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119 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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120 --best="${singlePaired.pParams.pBestOption.pBest}"
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121 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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122 --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}"
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123 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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124 #else:
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125 --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}"
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126 #end if
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127 --offrate="${singlePaired.pParams.pOffrate}"
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128 --seed="${singlePaired.pParams.pSeed}"
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129 #end if
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130 #end if
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131 </command>
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132 <inputs>
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133 <conditional name="refGenomeSource">
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134 <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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135 <option value="indexed">Use a built-in index</option>
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136 <option value="history">Use one from the history</option>
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137 </param>
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138 <when value="indexed">
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139 <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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140 <options from_data_table="bowtie_indexes">
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141 <filter type="sort_by" column="2" />
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142 <validator type="no_options" message="No indexes are available" />
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143 </options>
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144 </param>
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145 </when>
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146 <when value="history">
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147 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
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148 <conditional name="indexParams">
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149 <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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150 <option value="indexPreSet">Default</option>
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151 <option value="indexFull">Set your own</option>
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152 </param>
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153 <when value="indexPreSet" />
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154 <when value="indexFull">
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155 <conditional name="autoBehavior">
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156 <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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157 <option value="auto">Automatic behavior</option>
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158 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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159 </param>
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160 <when value="auto" />
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161 <when value="set">
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162 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
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163 <option value="unpacked">Use regular representation</option>
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164 <option value="packed">Use packed representation</option>
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165 </param>
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166 <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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167 <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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168 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
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169 </when>
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170 </conditional>
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171 <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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172 <option value="dc">Use difference-cover sample</option>
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173 <option value="nodc">Disable difference-cover sample</option>
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174 </param>
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175 <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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176 <option value="ref">Build all index files</option>
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parents:
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177 <option value="noref">Do not build paired-end alignment index files</option>
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178 </param>
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parents:
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179 <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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180 <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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parents:
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181 <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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182 <option value="no">Do not convert Ns</option>
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shantanu
parents:
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183 <option value="yes">Convert Ns to As</option>
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shantanu
parents:
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184 </param>
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parents:
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185 <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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parents:
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186 <option value="little">Little</option>
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shantanu
parents:
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187 <option value="big">Big</option>
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parents:
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188 </param>
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parents:
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189 <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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parents:
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190 <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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parents:
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191 </when> <!-- indexFull -->
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shantanu
parents:
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192 </conditional> <!-- indexParams -->
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shantanu
parents:
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193 </when> <!-- history -->
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shantanu
parents:
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194 </conditional> <!-- refGenomeSource -->
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shantanu
parents:
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195 <conditional name="singlePaired">
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parents:
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196 <param name="sPaired" type="select" label="Is this library mate-paired?">
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parents:
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197 <option value="single">Single-end</option>
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shantanu
parents:
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198 <option value="paired">Paired-end</option>
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shantanu
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199 </param>
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shantanu
parents:
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200 <when value="single">
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201 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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202 <conditional name="sParams">
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parents:
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203 <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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204 <option value="preSet">Commonly used</option>
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205 <option value="full">Full parameter list</option>
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parents:
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206 </param>
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shantanu
parents:
diff changeset
207 <when value="preSet" />
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shantanu
parents:
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208 <when value="full">
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209 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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210 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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211 <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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212 <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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213 <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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214 <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
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215 <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
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216 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
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217 <option value="round">Round to nearest 10</option>
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218 <option value="noRound">Do not round to nearest 10</option>
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219 </param>
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220 <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
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221 <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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222 <option value="noTryHard">Do not try hard</option>
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parents:
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223 <option value="doTryHard">Try hard</option>
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224 </param>
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225 <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
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parents:
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226 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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227 <option value="noAllValAligns">Do not report all valid alignments</option>
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228 <option value="doAllValAligns">Report all valid alignments</option>
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229 </param>
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230 <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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231 <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)" />
b8d21c7bb4e4 Uploaded
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232 <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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233 <conditional name="sBestOption">
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234 <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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235 <option value="noBest">Do not use best</option>
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236 <option value="doBest">Use best</option>
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shantanu
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237 </param>
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shantanu
parents:
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238 <when value="noBest">
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239 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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240 </when>
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241 <when value="doBest">
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242 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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243 <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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244 <option value="noStrata">Do not use strata option</option>
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245 <option value="doStrata">Use strata option</option>
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246 </param>
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247 </when>
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248 </conditional> <!-- bestOption -->
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249 <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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250 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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251 </when> <!-- full -->
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252 </conditional> <!-- sParams -->
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shantanu
parents:
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253 </when> <!-- single -->
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shantanu
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254 <when value="paired">
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255 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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256 <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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257 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
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shantanu
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258 <column name="name" index="0"/>
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shantanu
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259 <column name="value" index="0"/>
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shantanu
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260 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
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261 </options>
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262 </param>
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263 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
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264 <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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265 <option value="fr">FR (for Illumina)</option>
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266 <option value="rf">RF</option>
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267 <option value="ff">FF (for SOLiD)</option>
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268 </param>
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269 <conditional name="pParams">
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270 <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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271 <option value="preSet">Commonly used</option>
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272 <option value="full">Full parameter list</option>
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273 </param>
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shantanu
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274 <when value="preSet" />
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shantanu
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275 <when value="full">
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276 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
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277 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
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278 <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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shantanu
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279 <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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280 <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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shantanu
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281 <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
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282 <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
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283 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
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shantanu
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284 <option value="round">Round to nearest 10</option>
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285 <option value="noRound">Do not round to nearest 10</option>
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286 </param>
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287 <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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288 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
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289 <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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290 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)">
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291 <option value="forward">Align against the forward reference strand</option>
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shantanu
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292 <option value="noForward">Do not align against the forward reference strand</option>
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293 </param>
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294 <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
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295 <option value="reverse">Align against the reverse-complement reference strand</option>
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shantanu
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296 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
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297 </param>
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298 <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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299 <option value="noTryHard">Do not try hard</option>
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300 <option value="doTryHard">Try hard</option>
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301 </param>
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302 <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
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shantanu
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303 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
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shantanu
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304 <option value="noAllValAligns">Do not report all valid alignments</option>
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shantanu
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305 <option value="doAllValAligns">Report all valid alignments</option>
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306 </param>
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307 <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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308 <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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309 <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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310 <conditional name="pBestOption">
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311 <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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312 <option value="noBest">Do not use best</option>
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313 <option value="doBest">Use best</option>
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314 </param>
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315 <when value="noBest">
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316 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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317 </when>
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318 <when value="doBest">
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319 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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320 <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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shantanu
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321 <option value="noStrata">Do not use strata option</option>
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shantanu
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322 <option value="doStrata">Use strata option</option>
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shantanu
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323 </param>
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324 </when>
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325 </conditional>
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shantanu
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326 <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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shantanu
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diff changeset
327 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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shantanu
parents:
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328 </when> <!-- full -->
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parents:
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329 </conditional> <!-- pParams -->
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parents:
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330 </when> <!-- paired -->
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parents:
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331 </conditional> <!-- singlePaired -->
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parents:
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332 <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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parents:
diff changeset
333 </inputs>
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parents:
diff changeset
334 <outputs>
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335 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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parents:
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336 <actions>
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parents:
diff changeset
337 <conditional name="refGenomeSource.genomeSource">
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shantanu
parents:
diff changeset
338 <when value="indexed">
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parents:
diff changeset
339 <action type="metadata" name="dbkey">
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parents:
diff changeset
340 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
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parents:
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341 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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parents:
diff changeset
342 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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343 </option>
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344 </action>
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diff changeset
345 </when>
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parents:
diff changeset
346 <when value="history">
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parents:
diff changeset
347 <action type="metadata" name="dbkey">
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parents:
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348 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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349 </action>
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350 </when>
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351 </conditional>
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352 </actions>
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353 </data>
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354 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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parents:
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355 <filter>((
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parents:
diff changeset
356 singlePaired['sPaired'] == "single" and
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parents:
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357 singlePaired['sParams']['sSettingsType'] == "full" and
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parents:
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358 singlePaired['sParams']['sMaxFile'] is True
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parents:
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359 ) or (
b8d21c7bb4e4 Uploaded
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parents:
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360 singlePaired['sPaired'] == "paired" and
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361 singlePaired['pParams']['pSettingsType'] == "full" and
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parents:
diff changeset
362 singlePaired['pParams']['pMaxFile'] is True
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parents:
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363 ))
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364 </filter>
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parents:
diff changeset
365 <actions>
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366 <conditional name="singlePaired.sPaired">
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parents:
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367 <when value="single">
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368 <action type="format">
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369 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
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370 </action>
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371 </when>
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372 <when value="paired">
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parents:
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373 <action type="format">
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parents:
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374 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
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375 </action>
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376 </when>
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377 </conditional>
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378 </actions>
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379 </data>
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parents:
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380 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
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parents:
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381 <filter>singlePaired['sPaired'] == "paired"</filter>
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shantanu
parents:
diff changeset
382 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
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shantanu
parents:
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383 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
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shantanu
parents:
diff changeset
384 <actions>
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shantanu
parents:
diff changeset
385 <conditional name="singlePaired.sPaired">
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shantanu
parents:
diff changeset
386 <when value="single">
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shantanu
parents:
diff changeset
387 <action type="format">
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shantanu
parents:
diff changeset
388 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
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shantanu
parents:
diff changeset
389 </action>
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shantanu
parents:
diff changeset
390 </when>
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shantanu
parents:
diff changeset
391 <when value="paired">
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shantanu
parents:
diff changeset
392 <action type="format">
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shantanu
parents:
diff changeset
393 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
394 </action>
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parents:
diff changeset
395 </when>
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shantanu
parents:
diff changeset
396 </conditional>
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shantanu
parents:
diff changeset
397 </actions>
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shantanu
parents:
diff changeset
398 </data>
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shantanu
parents:
diff changeset
399 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
400 <filter>
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shantanu
parents:
diff changeset
401 ((
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
402 singlePaired['sPaired'] == "single" and
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
403 singlePaired['sParams']['sSettingsType'] == "full" and
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
404 singlePaired['sParams']['sUnmappedFile'] is True
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
405 ) or (
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
406 singlePaired['sPaired'] == "paired" and
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
407 singlePaired['pParams']['pSettingsType'] == "full" and
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
408 singlePaired['pParams']['pUnmappedFile'] is True
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
409 ))
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
410 </filter>
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shantanu
parents:
diff changeset
411 <actions>
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shantanu
parents:
diff changeset
412 <conditional name="singlePaired.sPaired">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
413 <when value="single">
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shantanu
parents:
diff changeset
414 <action type="format">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
415 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
416 </action>
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shantanu
parents:
diff changeset
417 </when>
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shantanu
parents:
diff changeset
418 <when value="paired">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
419 <action type="format">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
420 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
421 </action>
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shantanu
parents:
diff changeset
422 </when>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
423 </conditional>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
424 </actions>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
425 </data>
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shantanu
parents:
diff changeset
426 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
427 <filter>singlePaired['sPaired'] == "paired"</filter>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
428 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
429 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
430 <actions>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
431 <conditional name="singlePaired.sPaired">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
432 <when value="single">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
433 <action type="format">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
434 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
435 </action>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
436 </when>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
437 <when value="paired">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
438 <action type="format">
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
439 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
440 </action>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
441 </when>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
442 </conditional>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
443 </actions>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
444 </data>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
445 </outputs>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
446 <tests>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
447 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
448 <!--
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
449 Bowtie command:
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
450 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
451 sort bowtie_out6_u.sam > bowtie_out6.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
452 -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
453 chrM_base needs to be the base location/name of the index files.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
454 -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
455 <param name="genomeSource" value="indexed" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
456 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
457 <param name="index" value="equCab2chrM" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
458 <param name="sPaired" value="single" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
459 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
460 <param name="sSettingsType" value="preSet" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
461 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
462 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
463 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
464 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
465 <!--
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
466 Bowtie command:
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
467 bowtie-build -f test-data/phiX.fasta phiX_base
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
468 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
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
469 sort bowtie_out7_u.sam > bowtie_out7.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
470 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
471 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
472 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
473 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
474 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
475 chrM_base is the index files' location/base name.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
476 -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
477 <param name="genomeSource" value="history" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
478 <param name="ownFile" value="phiX.fasta" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
479 <param name="indexSettings" value="indexPreSet" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
480 <param name="sPaired" value="paired" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
481 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
482 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
483 <param name="pMaxInsert" value="1000" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
484 <param name="pMateOrient" value="ff" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
485 <param name="pSettingsType" value="full" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
486 <param name="pSkip" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
487 <param name="pAlignLimit" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
488 <param name="pTrimH" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
489 <param name="pTrimL" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
490 <param name="pMismatchSeed" value="2" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
491 <param name="pMismatchQual" value="70" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
492 <param name="pSeedLen" value="28" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
493 <param name="pRounding" value="round" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
494 <param name="pMaqSoapAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
495 <param name="pMinInsert" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
496 <param name="pMaxAlignAttempt" value="100" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
497 <param name="pForwardAlign" value="forward" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
498 <param name="pReverseAlign" value="reverse" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
499 <param name="pTryHard" value="noTryHard" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
500 <param name="pValAlign" value="1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
501 <param name="pAllValAligns" value="noAllValAligns" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
502 <param name="pSuppressAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
503 <param name="pUnmappedFile" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
504 <param name="pMaxFile" value="false" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
505 <param name="pBest" value="doBest" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
506 <param name="pdMaxBacktracks" value="800" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
507 <param name="pdStrata" value="noStrata" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
508 <param name="pOffrate" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
509 <param name="pSeed" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
510 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
511 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
512 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
513 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
514 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
515 <!-- start testing of non-sanger variant fastq reads -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
516 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
517 <param name="genomeSource" value="history" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
518 <param name="ownFile" value="phiX.fasta" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
519 <param name="indexSettings" value="indexPreSet" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
520 <param name="sPaired" value="paired" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
521 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
522 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
523 <param name="pMaxInsert" value="1000" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
524 <param name="pMateOrient" value="ff" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
525 <param name="pSettingsType" value="full" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
526 <param name="pSkip" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
527 <param name="pAlignLimit" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
528 <param name="pTrimH" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
529 <param name="pTrimL" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
530 <param name="pMismatchSeed" value="2" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
531 <param name="pMismatchQual" value="70" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
532 <param name="pSeedLen" value="28" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
533 <param name="pRounding" value="round" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
534 <param name="pMaqSoapAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
535 <param name="pMinInsert" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
536 <param name="pMaxAlignAttempt" value="100" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
537 <param name="pForwardAlign" value="forward" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
538 <param name="pReverseAlign" value="reverse" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
539 <param name="pTryHard" value="noTryHard" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
540 <param name="pValAlign" value="1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
541 <param name="pAllValAligns" value="noAllValAligns" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
542 <param name="pSuppressAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
543 <param name="pUnmappedFile" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
544 <param name="pMaxFile" value="false" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
545 <param name="pBest" value="doBest" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
546 <param name="pdMaxBacktracks" value="800" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
547 <param name="pdStrata" value="noStrata" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
548 <param name="pOffrate" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
549 <param name="pSeed" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
550 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
551 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
552 <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
553 <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
554 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
555 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
556 <param name="genomeSource" value="history" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
557 <param name="ownFile" value="phiX.fasta" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
558 <param name="indexSettings" value="indexPreSet" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
559 <param name="sPaired" value="paired" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
560 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
561 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
562 <param name="pMaxInsert" value="1000" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
563 <param name="pMateOrient" value="ff" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
564 <param name="pSettingsType" value="full" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
565 <param name="pSkip" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
566 <param name="pAlignLimit" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
567 <param name="pTrimH" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
568 <param name="pTrimL" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
569 <param name="pMismatchSeed" value="2" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
570 <param name="pMismatchQual" value="70" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
571 <param name="pSeedLen" value="28" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
572 <param name="pRounding" value="round" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
573 <param name="pMaqSoapAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
574 <param name="pMinInsert" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
575 <param name="pMaxAlignAttempt" value="100" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
576 <param name="pForwardAlign" value="forward" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
577 <param name="pReverseAlign" value="reverse" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
578 <param name="pTryHard" value="noTryHard" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
579 <param name="pValAlign" value="1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
580 <param name="pAllValAligns" value="noAllValAligns" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
581 <param name="pSuppressAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
582 <param name="pUnmappedFile" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
583 <param name="pMaxFile" value="false" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
584 <param name="pBest" value="doBest" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
585 <param name="pdMaxBacktracks" value="800" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
586 <param name="pdStrata" value="noStrata" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
587 <param name="pOffrate" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
588 <param name="pSeed" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
589 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
590 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
591 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
592 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
593 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
594 <!-- end testing of non-sanger variant fastq reads -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
595 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
596 <!--
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
597 Bowtie command:
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
598 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
599 sort bowtie_out9_u.sam > bowtie_out9.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
600 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
601 chrM_base is the index files' location/base name.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
602 -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
603 <param name="genomeSource" value="indexed" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
604 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
605 <param name="index" value="equCab2chrM" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
606 <param name="sPaired" value="single" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
607 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
608 <param name="sSettingsType" value="full" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
609 <param name="sSkip" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
610 <param name="sAlignLimit" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
611 <param name="sTrimH" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
612 <param name="sTrimL" value="0" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
613 <param name="sMismatchSeed" value="2" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
614 <param name="sMismatchQual" value="70" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
615 <param name="sSeedLen" value="28" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
616 <param name="sRounding" value="round" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
617 <param name="sMaqSoapAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
618 <param name="sTryHard" value="doTryHard" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
619 <param name="sValAlign" value="1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
620 <param name="sAllValAligns" value="noAllValAligns" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
621 <param name="sSuppressAlign" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
622 <param name="sUnmappedFile" value="false" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
623 <param name="sMaxFile" value="false" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
624 <param name="sBest" value="noBest" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
625 <param name="snMaxBacktracks" value="125" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
626 <param name="sOffrate" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
627 <param name="sSeed" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
628 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
629 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
630 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
631 <test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
632 <!--
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
633 Bowtie command:
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
634 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
635 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
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
636 sort bowtie_out10_u.sam > bowtie_out10.sam
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
637 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
638 chrM_base is the index files' location/base name.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
639 -->
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
640 <param name="genomeSource" value="history" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
641 <param name="ownFile" value="phiX.fasta" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
642 <param name="indexSettings" value="indexFull" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
643 <param name="autoB" value="auto" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
644 <param name="nodc" value="dc" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
645 <param name="noref" value="ref" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
646 <param name="offrate" value="5" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
647 <param name="ftab" value="10" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
648 <param name="ntoa" value="no" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
649 <param name="endian" value="little" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
650 <param name="seed" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
651 <param name="cutoff" value="-1" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
652 <param name="sPaired" value="paired" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
653 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
654 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
655 <param name="pMaxInsert" value="1000" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
656 <param name="pMateOrient" value="ff" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
657 <param name="pSettingsType" value="preSet" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
658 <param name="suppressHeader" value="true" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
659 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
660 </test>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
661 </tests>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
662
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
663 <help>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
664
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
665 **What it does**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
666
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
667 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.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
668
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
669 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
670
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
671 ------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
672
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
673 **Know what you are doing**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
674
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
675 .. class:: warningmark
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
676
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
677 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.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
678
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
679 .. __: http://bowtie-bio.sourceforge.net/index.shtml
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
680
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
681 ------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
682
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
683 **Input formats**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
684
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
685 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
686
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
687 ------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
688
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
689 **A Note on Built-in Reference Genomes**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
690
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
691 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.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
692
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
693 ------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
694
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
695 **Outputs**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
696
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
697 The output is in SAM format, and has the following columns::
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
698
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
699 Column Description
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
700 -------- --------------------------------------------------------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
701 1 QNAME Query (pair) NAME
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
702 2 FLAG bitwise FLAG
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
703 3 RNAME Reference sequence NAME
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
704 4 POS 1-based leftmost POSition/coordinate of clipped sequence
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
705 5 MAPQ MAPping Quality (Phred-scaled)
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
706 6 CIGAR extended CIGAR string
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
707 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
708 8 MPOS 1-based Mate POSition
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
709 9 ISIZE Inferred insert SIZE
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
710 10 SEQ query SEQuence on the same strand as the reference
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
711 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
712 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
713
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
714 The flags are as follows::
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
715
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
716 Flag Description
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
717 ------ -------------------------------------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
718 0x0001 the read is paired in sequencing
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
719 0x0002 the read is mapped in a proper pair
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
720 0x0004 the query sequence itself is unmapped
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
721 0x0008 the mate is unmapped
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
722 0x0010 strand of the query (1 for reverse)
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
723 0x0020 strand of the mate
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
724 0x0040 the read is the first read in a pair
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
725 0x0080 the read is the second read in a pair
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
726 0x0100 the alignment is not primary
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
727
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
728 It looks like this (scroll sideways to see the entire example)::
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
729
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
730 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
731 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
732 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
733
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
734 -------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
735
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
736 **Bowtie settings**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
737
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
738 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
739
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
740 ------
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
741
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
742 **Bowtie parameter list**
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
743
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
744 This is an exhaustive list of Bowtie options:
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
745
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
746 For indexing (bowtie-build)::
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
747
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
748 -a No auto behavior. Disable the default behavior where bowtie automatically
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
749 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
750 to the memory available. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
751 --packed Packing. Use a packed representation for DNA strings. [auto]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
752 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
753 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
754 expressed as a fraction of the length of the reference. [4]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
755 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
756 sample. [1024]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
757 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
758 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
759 of the index. Used only for paired-end alignment. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
760 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
761 indexer will mark every 2^INT rows. The marked rows correspond to rows on
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
762 the genome. [5]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
763 -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
764 with respect to the first INT characters of the query. Ftab is 4^INT+1
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
765 bytes. [10]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
766 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
767 simply excluded from the index and Bowtie will not find alignments that
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
768 overlap them. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
769 --big Endianness. Endianness to use when serializing integers to the index file. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
770 --little Endianness. [--little]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
771 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
772 --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
773 across sequences) and ignore the rest. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
774
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
775 For aligning (bowtie)::
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
776
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
777 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
778 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
779 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
780 read before alignment. [0]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
781 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
782 read before alignment. [0]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
783 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
784 with seed length option). Can be 0, 1, 2, or 3. [2]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
785 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
786 read positions. Bowtie rounds quality values to the nearest 10 and saturates
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
787 at 30. [70]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
788 -l INT Seed length. The number of bases on the high-quality end of the read to
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
789 which the -n ceiling applies. Must be at least 5. [28]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
790 --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
791 saturate at 30. This options turns off that rounding. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
792 -v INT MAQ- or SOAP-like alignment policy. This option turns off the default
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
793 MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
794 with at most INT mismatches. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
795 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
796 Does checking on untrimmed reads if -5 or -3 is used. [0]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
797 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
798 Does checking on untrimmed reads if -5 or -3 is used. [250]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
799 --fr Mate orientation. The upstream/downstream mate orientations for a valid
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
800 paired-end alignment against the forward reference strand. [--fr]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
801 --rf Mate orientation. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
802 --ff Mate orientation. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
803 --pairtries INT Maximum alignment attempts for paired-end data. [100]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
804 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
805 to align against the forward reference strand. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
806 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
807 attempt to align against the reverse-complement reference strand. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
808 --un FILENAME Write all reads that could not be aligned to file [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
809 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
810 set with the -m option to file [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
811 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
812 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
813 -y Try hard. Try as hard as possible to find valid alignments when they exist,
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
814 including paired-end alignments. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
815 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
816 store path descriptors in --best mode. [32]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
817 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
818 -a All valid alignments. Choosing this means that all valid alignments per read
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
819 or pair will be reported. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
820 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
821 if more than INT reportable alignments exist for it. [no limit]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
822 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
823 "best" in terms of stratum (the number of mismatches) and quality values at
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
824 mismatched position. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
825 --strata Best strata. When running in best mode, report alignments that fall into the
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
826 best stratum if there are ones falling into more than one. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
827 -o INT Offrate override. Override the offrate of the index with INT. Some row
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
828 markings are discarded when index read into memory. INT must be greater than
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
829 the value used to build the index (default: 5). [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
830 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
831 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
832 SNPs per base in the subject genome. [see --snpfrac]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
833 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
834 alignments. [0.001]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
835 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
836 alignments. [off]
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
837
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
838 </help>
b8d21c7bb4e4 Uploaded
shantanu
parents:
diff changeset
839 </tool>