annotate bismark_bowtie2_wrapper.xml @ 5:b100248c35b8 draft

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author bgruening
date Mon, 09 Feb 2015 18:27:40 -0500
parents 243e8f9fb75b
children 0f8646f22b8d
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1 <tool id="bismark_bowtie2" name="Bismark" version="0.10.2">
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2 <!-- Wrapper compatible with Bismark version 0.10 -->
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3 <description>bisulfite mapper (bowtie2)</description>
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4 <!--<version_command>bismark version</version_command>-->
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5 <requirements>
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6 <requirement type="set_environment">SCRIPT_PATH</requirement>
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82814a8a2395 added samtools 0.1.19 as dependency
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7 <requirement type="package" version="0.1.19">samtools</requirement>
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8 <requirement type="package" version="2.1.0">bowtie2</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 <exit_code range=":-1" />
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13 <regex match="Error:" />
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14 <regex match="Exception:" />
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15 </stdio>
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16 <command interpreter="python">
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17 <![CDATA[
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18 bismark_wrapper.py
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19
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20 ## Change this to accommodate the number of threads you have available.
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21 --num-threads "\${GALAXY_SLOTS:-24}"
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22
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23 ##--bismark_path \$SCRIPT_PATH
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24
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25 --bowtie2
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26
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27 ##
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28 ## Bismark Genome Preparation, if desired.
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29 ##
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30
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31 ## Handle reference file.
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32 #if $refGenomeSource.genomeSource == "history":
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33 --own-file=$refGenomeSource.ownFile
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34 #else:
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35 --indexes-path ${refGenomeSource.index.fields.path}
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36 #end if
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37
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38
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39 ##
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40 ## Input parameters
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41 ##
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42
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43 #if $singlePaired.sPaired == "single":
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44 --single-paired $singlePaired.input_singles
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45
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46 #if $singlePaired.input_singles.ext == "fastqillumina":
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47 --phred64-quals
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48 --fastq
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49 #elif $singlePaired.input_singles.ext == "fastqsanger":
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50 --fastq
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51 #elif $singlePaired.input_singles.ext == "fasta":
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52 --fasta
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53 #end if
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54 #else:
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55 --mate-paired
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56 #set $mate1 = list()
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57 #set $mate2 = list()
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58 #for $mate_pair in $singlePaired.mate_list
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59 $mate1.append( str($mate_pair.input_mate1) )
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60 $mate2.append( str($mate_pair.input_mate2) )
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61 #end for
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62
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63 --mate1 #echo ','.join($mate1)
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64 --mate2 #echo ','.join($mate2)
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65
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66 #for $mate_pair in $singlePaired.mate_list:
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67 #if $mate_pair.input_mate1.ext == "fastqillumina":
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68 --phred64-quals
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69 --fastq
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70 #elif $mate_pair.input_mate1.ext == "fastqsanger":
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71 --fastq
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72 #elif $mate_pair.input_mate1.ext == "fasta":
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73 --fasta
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74 #end if
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75 #break
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76 #end for
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77
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78 -I $singlePaired.minInsert
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79 -X $singlePaired.maxInsert
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80 #end if
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81
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82 #if $sort_bam:
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83 --sort-bam
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84 #end if
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85
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86 ## for now hardcode the value for the required memory per thread in --best mode
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87 --chunkmbs 512
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88
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89
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90 #if $params.settingsType == "custom":
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91
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92 ## default 20
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93 --seed-len $params.seed_len
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94 ## default 0
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95 --seed-mismatches $params.seed_mismatches
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96 ## default 15
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97 --seed-extention-attempts $params.seed_extention_attempts
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98 ## default 2
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99 --max-reseed $params.max_reseed
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100
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101 ## default 70
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102 ##--maqerr $params.maqerr
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103
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104 ## default unlimited
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105 #if $params.qupto != 0:
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106 --qupto $params.qupto
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107 #end if
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108 #if $params.skip_reads != 0:
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109 --skip-reads $params.skip_reads
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110 #end if
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111
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112 ## if set, disable the original behaviour
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113 $params.no_mixed
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114 ## if set, disable the original behaviour
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115 $params.no_discordant
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116
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117 #if $params.bismark_stdout:
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118 --stdout $output_stdout
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119 #end if
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120
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121 #if $params.isReportOutput:
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122 --output-report-file $report_file
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123 #end if
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124
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125 #end if
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126
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127 ##
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128 ## Output parameters.
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129 ##
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130 --output $output
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131 ##$suppress_header
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132
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133 #if str( $singlePaired.sPaired ) == "single"
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134 #if $output_unmapped_reads_l
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135 --output-unmapped-reads $output_unmapped_reads_l
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136 #end if
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137 #if $output_suppressed_reads_l
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parents:
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138 --output-suppressed-reads $output_suppressed_reads_l
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139 #end if
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140 #else
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141 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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parents:
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142 --output-unmapped-reads-l $output_unmapped_reads_l
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143 --output-unmapped-reads-r $output_unmapped_reads_r
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144 #end if
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145 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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146 --output-suppressed-reads-l $output_suppressed_reads_l
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147 --output-suppressed-reads-r $output_suppressed_reads_r
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148 #end if
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149 #end if
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150
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151 ]]>
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152 </command>
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153 <inputs>
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154 <conditional name="refGenomeSource">
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155 <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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156 <option value="indexed">Use a built-in index</option>
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157 <option value="history">Use one from the history</option>
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158 </param>
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159 <when value="indexed">
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160 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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161 <options from_data_table="bowtie2_indexes">
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162 <filter type="sort_by" column="2"/>
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163 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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164 </options>
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165 </param>
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166 </when> <!-- build-in -->
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167 <when value="history">
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168 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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169 </when> <!-- history -->
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170 </conditional> <!-- refGenomeSource -->
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171
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172 <!-- Input Parameters -->
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173 <conditional name="singlePaired">
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174 <param name="sPaired" type="select" label="Is this library mate-paired?">
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175 <option value="single">Single-end</option>
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176 <option value="paired">Paired-end</option>
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177 </param>
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178 <when value="single">
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179 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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180 </when>
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181 <when value="paired">
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182 <repeat name="mate_list" title="Paired End Pairs" min="1">
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183 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
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184 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
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185 </repeat>
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186 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
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187 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
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188 </when>
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189 </conditional>
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190
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191 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
0
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192
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193 <conditional name="params">
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194 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
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195 <option value="default">Use Defaults</option>
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196 <option value="custom">Full parameter list</option>
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197 </param>
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198 <when value="default" />
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199 <!-- Full/advanced params. -->
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200 <when value="custom">
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201 <!-- -N -->
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202 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
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parents:
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203 <!-- -L -->
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204 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
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205 <!--
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206 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
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207 -->
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208 <!-- -D -->
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209 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
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210 <!-- -R -->
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211 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
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212
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213 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
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214 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
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215
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216 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
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217 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
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218
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219 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
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220 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" />
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221 <!-- output Options -->
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222 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
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223 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
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224
4
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225 <!--end output options -->
0
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226 </when> <!-- full -->
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227 </conditional> <!-- params -->
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228 <!--
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229 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" 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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230 -->
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231 </inputs>
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232
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233
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234 <outputs>
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235 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
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236 <filter>
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237 ((
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238 params['settingsType'] == "custom" and
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239 params['isReportOutput'] is True
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240 ))
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241 </filter>
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242 </data>
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243 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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244 <filter>
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245 ((
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246 params['settingsType'] == "custom" and
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247 params['bismark_stdout'] is True
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248 ))
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249 </filter>
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250 </data>
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251
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252 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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253 <actions>
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254 <conditional name="refGenomeSource.genomeSource">
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255 <when value="indexed">
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256 <action type="metadata" name="dbkey">
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257 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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258 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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259 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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260 </option>
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261 </action>
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262 </when>
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263 <when value="history">
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264 <action type="metadata" name="dbkey">
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265 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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266 </action>
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267 </when>
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268 </conditional>
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269 </actions>
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270 </data>
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271
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272 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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273 <filter>
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274 ((
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275 params['settingsType'] == "custom" and
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276 params['suppressed_read_file'] is True
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277 ))
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278 </filter>
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279 <actions>
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280 <conditional name="singlePaired.sPaired">
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281 <when value="single">
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282 <action type="format">
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283 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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284 </action>
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285 </when>
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286 <when value="paired">
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287 <!--action type="format">
0
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288 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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289 </action-->
0
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290 </when>
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291 </conditional>
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292 </actions>
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293 </data>
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294
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295 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
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296 <filter>
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297 ((
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298 singlePaired['sPaired'] == "paired" and
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299 params['settingsType'] == "custom" and
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300 params['suppressed_read_file'] is True
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301 ))
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parents: 3
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302 </filter>
0
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303 <actions>
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304 <conditional name="singlePaired.sPaired">
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305 <when value="single">
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306 <action type="format">
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307 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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308 </action>
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309 </when>
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310 <when value="paired">
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311 <!--action type="format">
0
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312 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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313 </action-->
0
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314 </when>
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315 </conditional>
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316 </actions>
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317 </data>
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318
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319 <!-- Outout unmapped reads -->
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320 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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321 <filter>
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322 ((
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323 params['settingsType'] == "custom" and
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324 params['unmapped_read_file'] is True
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325 ))
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326 </filter>
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327 <actions>
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328 <conditional name="singlePaired.sPaired">
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329 <when value="single">
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330 <action type="format">
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331 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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332 </action>
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333 </when>
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334 <when value="paired">
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335 <!--action type="format">
0
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336 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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337 </action-->
0
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338 </when>
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339 </conditional>
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340 </actions>
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341 </data>
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342
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343 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
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344 <filter>
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345 ((
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346 singlePaired['sPaired'] == "paired" and
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347 params['settingsType'] == "custom" and
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348 params['unmapped_read_file'] is True
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349 ))
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350 </filter>
0
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351 <actions>
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352 <conditional name="singlePaired.sPaired">
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353 <when value="single">
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354 <action type="format">
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355 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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356 </action>
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357 </when>
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358 <when value="paired">
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359 <!--action type="format">
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360 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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361 </action-->
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362 </when>
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363 </conditional>
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364 </actions>
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365 </data>
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366 </outputs>
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367
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368 <tests>
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369 </tests>
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370
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parents:
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371 <help>
4
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372 <![CDATA[
0
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parents:
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373
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parents:
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374 **What it does**
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375
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376 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
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377 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
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378 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
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379 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
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380 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
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parents:
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381 forward strand, by doing this alignments will produce the same positions). These instances of Bowtie 2
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382 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
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383 sequence from the genome and determine if there were any protected C's present or not.
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384
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parents:
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385 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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386
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387 As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
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388 re-enabled by using non_directional mode.
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389
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390 It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
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parents:
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391
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parents:
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392 ------
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parents:
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393
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parents:
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394 **Know what you are doing**
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parents:
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395
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parents:
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396 .. class:: warningmark
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397
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parents:
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398 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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parents:
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399
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400 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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401
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parents:
diff changeset
402
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parents:
diff changeset
403 .. class:: warningmark
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parents:
diff changeset
404
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parents:
diff changeset
405 Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
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parents:
diff changeset
406
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parents:
diff changeset
407 ------
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parents:
diff changeset
408
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parents:
diff changeset
409 **Input formats**
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parents:
diff changeset
410
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parents:
diff changeset
411 Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
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parents:
diff changeset
412
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parents:
diff changeset
413 ------
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parents:
diff changeset
414
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parents:
diff changeset
415 **A Note on Built-in Reference Genomes**
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parents:
diff changeset
416
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parents:
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417 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.
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parents:
diff changeset
418
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parents:
diff changeset
419 ------
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parents:
diff changeset
420
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parents:
diff changeset
421 The final output of Bismark is in SAM format by default.
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parents:
diff changeset
422
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parents:
diff changeset
423 **Outputs**
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parents:
diff changeset
424
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parents:
diff changeset
425 The output is in SAM format, and has the following columns::
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parents:
diff changeset
426
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parents:
diff changeset
427 Column Description
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parents:
diff changeset
428 -------- --------------------------------------------------------
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parents:
diff changeset
429 1 QNAME seq-ID
4
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parents: 3
diff changeset
430 2 FLAG this flag tries to take the strand a bisulfite read
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parents: 3
diff changeset
431 originated from into account
0
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parents:
diff changeset
432 (this is different from ordinary DNA alignment flags!)
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parents:
diff changeset
433 3 RNAME chromosome
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parents:
diff changeset
434 4 POS start position
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parents:
diff changeset
435 5 MAPQ always 255
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parents:
diff changeset
436 6 CIGAR extended CIGAR string
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parents:
diff changeset
437 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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parents:
diff changeset
438 8 MPOS 1-based Mate POSition
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parents:
diff changeset
439 9 ISIZE Inferred insert SIZE
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parents:
diff changeset
440 10 SEQ query SEQuence on the same strand as the reference
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parents:
diff changeset
441 11 QUAL Phred33 scale
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parents:
diff changeset
442 12 NM-tag edit distance to the reference)
4
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parents: 3
diff changeset
443 13 XX-tag base-by-base mismatches to the reference.
0
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parents:
diff changeset
444 This does not include indels.
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parents:
diff changeset
445 14 XM-tag methylation call string
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parents:
diff changeset
446 15 XR-tag read conversion state for the alignment
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parents:
diff changeset
447 16 XG-tag genome conversion state for the alignment
4
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parents: 3
diff changeset
448
0
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parents:
diff changeset
449
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parents:
diff changeset
450 Each read of paired-end alignments is written out in a separate line in the above format.
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parents:
diff changeset
451
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parents:
diff changeset
452
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parents:
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453 It looks like this (scroll sideways to see the entire example)::
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parents:
diff changeset
454
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parents:
diff changeset
455 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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parents:
diff changeset
456 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
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parents:
diff changeset
457 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
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parents:
diff changeset
458
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parents:
diff changeset
459 -------
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parents:
diff changeset
460
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parents:
diff changeset
461 **Bismark settings**
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parents:
diff changeset
462
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parents:
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463 All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
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parents:
diff changeset
464
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parents:
diff changeset
465 ------
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parents:
diff changeset
466
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parents:
diff changeset
467 **Bismark parameter list**
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parents:
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468
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parents:
diff changeset
469 This is an exhaustive list of Bismark options.
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parents:
diff changeset
470
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parents:
diff changeset
471 Input::
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parents:
diff changeset
472
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parents:
diff changeset
473 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
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parents:
diff changeset
474 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
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parents:
diff changeset
475 produce one mapping result and one report file per input file.
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parents:
diff changeset
476
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parents:
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477 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
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parents:
diff changeset
478 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
479 correspond file-for-file and read-for-read with those specified in mates2.
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parents:
diff changeset
480 Reads may be a mix of different lengths. Bismark will produce one mapping result
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parents:
diff changeset
481 and one report file per paired-end input file pair.
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parents:
diff changeset
482
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parents:
diff changeset
483 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
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parents:
diff changeset
484 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
485 correspond file-for-file and read-for-read with those specified in mates1.
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parents:
diff changeset
486 Reads may be a mix of different lengths.
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parents:
diff changeset
487
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parents:
diff changeset
488 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
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parents:
diff changeset
489 files (usually having extension .fg or .fastq). This is the default. See also
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parents:
diff changeset
490 --solexa-quals.
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parents:
diff changeset
491
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parents:
diff changeset
492 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
62c6da72dd4a Uploaded
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parents:
diff changeset
493 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
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parents:
diff changeset
494 are assumed to be 40 on the Phred scale.
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parents:
diff changeset
495
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parents:
diff changeset
496 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
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parents:
diff changeset
497
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parents:
diff changeset
498 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
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parents:
diff changeset
499
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parents:
diff changeset
500 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
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parents:
diff changeset
501
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parents:
diff changeset
502 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
62c6da72dd4a Uploaded
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parents:
diff changeset
503
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parents:
diff changeset
504 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
4
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parents: 3
diff changeset
505 (which can't). The formula for conversion is:
0
62c6da72dd4a Uploaded
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parents:
diff changeset
506 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
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parents:
diff changeset
507 is usually the right option for use with (unconverted) reads emitted by the GA
62c6da72dd4a Uploaded
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parents:
diff changeset
508 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
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parents:
diff changeset
509
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parents:
diff changeset
510 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
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parents:
diff changeset
511 reads emitted by GA Pipeline version 1.3 or later. Default: off.
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parents:
diff changeset
512
62c6da72dd4a Uploaded
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parents:
diff changeset
513
62c6da72dd4a Uploaded
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parents:
diff changeset
514 Alignment::
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parents:
diff changeset
515
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parents:
diff changeset
516 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
4
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parents: 3
diff changeset
517 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
0
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parents:
diff changeset
518 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
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parents:
diff changeset
519
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parents:
diff changeset
520 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
62c6da72dd4a Uploaded
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parents:
diff changeset
521 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
62c6da72dd4a Uploaded
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parents:
diff changeset
522 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
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parents:
diff changeset
523
62c6da72dd4a Uploaded
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parents:
diff changeset
524 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
62c6da72dd4a Uploaded
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parents:
diff changeset
525 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
62c6da72dd4a Uploaded
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parents:
diff changeset
526 quality values to the nearest 10 and saturates at 30. This value is not relevant for
62c6da72dd4a Uploaded
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parents:
diff changeset
527 Bowtie 2.
62c6da72dd4a Uploaded
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parents:
diff changeset
528
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parents:
diff changeset
529 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
62c6da72dd4a Uploaded
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parents:
diff changeset
530 --best mode. Best-first search must keep track of many paths at once to ensure it is
62c6da72dd4a Uploaded
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parents:
diff changeset
531 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
62c6da72dd4a Uploaded
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parents:
diff changeset
532 memory impact of the descriptors, but they can still grow very large in some cases. If
62c6da72dd4a Uploaded
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parents:
diff changeset
533 you receive an error message saying that chunk memory has been exhausted in --best mode,
62c6da72dd4a Uploaded
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parents:
diff changeset
534 try adjusting this parameter up to dedicate more memory to the descriptors. This value
62c6da72dd4a Uploaded
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parents:
diff changeset
535 is not relevant for Bowtie 2. Default: 512.
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parents:
diff changeset
536
62c6da72dd4a Uploaded
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parents:
diff changeset
537 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
62c6da72dd4a Uploaded
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parents:
diff changeset
538 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
62c6da72dd4a Uploaded
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parents:
diff changeset
539 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
62c6da72dd4a Uploaded
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parents:
diff changeset
540 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
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parents:
diff changeset
541
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parents:
diff changeset
542 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
62c6da72dd4a Uploaded
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parents:
diff changeset
543 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
62c6da72dd4a Uploaded
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parents:
diff changeset
544 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
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parents:
diff changeset
545 A 61-bp gap would not be valid in that case. Default: 500.
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parents:
diff changeset
546
62c6da72dd4a Uploaded
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parents:
diff changeset
547
62c6da72dd4a Uploaded
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parents:
diff changeset
548
62c6da72dd4a Uploaded
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parents:
diff changeset
549 Output::
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parents:
diff changeset
550
62c6da72dd4a Uploaded
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parents:
diff changeset
551 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
62c6da72dd4a Uploaded
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parents:
diff changeset
552 bisulfite strands will be reported. Default: OFF.
62c6da72dd4a Uploaded
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parents:
diff changeset
553
62c6da72dd4a Uploaded
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parents:
diff changeset
554 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
62c6da72dd4a Uploaded
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parents:
diff changeset
555 to the original strands are merely theoretical and should not exist in reality. Specifying directional
62c6da72dd4a Uploaded
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parents:
diff changeset
556 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
62c6da72dd4a Uploaded
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parents:
diff changeset
557 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
62c6da72dd4a Uploaded
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parents:
diff changeset
558 for sprand-specific libraries).
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parents:
diff changeset
559
62c6da72dd4a Uploaded
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parents:
diff changeset
560 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
62c6da72dd4a Uploaded
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parents:
diff changeset
561 split up into several smaller files to run concurrently and the output files are to be merged.
62c6da72dd4a Uploaded
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parents:
diff changeset
562
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parents:
diff changeset
563 --quiet Print nothing besides alignments.
62c6da72dd4a Uploaded
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parents:
diff changeset
564
62c6da72dd4a Uploaded
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parents:
diff changeset
565 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
62c6da72dd4a Uploaded
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parents:
diff changeset
566 of SAM format output.
62c6da72dd4a Uploaded
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parents:
diff changeset
567
62c6da72dd4a Uploaded
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parents:
diff changeset
568 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
62c6da72dd4a Uploaded
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parents:
diff changeset
569 appear as they did in the input, without any translation of quality values that may have
62c6da72dd4a Uploaded
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parents:
diff changeset
570 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
62c6da72dd4a Uploaded
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parents:
diff changeset
571 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
62c6da72dd4a Uploaded
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parents:
diff changeset
572 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
62c6da72dd4a Uploaded
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parents:
diff changeset
573 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
62c6da72dd4a Uploaded
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parents:
diff changeset
574
62c6da72dd4a Uploaded
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parents:
diff changeset
575 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
62c6da72dd4a Uploaded
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parents:
diff changeset
576 mismatches or other reads that fail to align uniquely to a file in the output directory.
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bgruening
parents:
diff changeset
577 Written reads will appear as they did in the input, without any of the translation of quality
62c6da72dd4a Uploaded
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parents:
diff changeset
578 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
62c6da72dd4a Uploaded
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parents:
diff changeset
579 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
62c6da72dd4a Uploaded
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parents:
diff changeset
580 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
62c6da72dd4a Uploaded
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parents:
diff changeset
581
62c6da72dd4a Uploaded
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parents:
diff changeset
582 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
62c6da72dd4a Uploaded
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parents:
diff changeset
583 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
62c6da72dd4a Uploaded
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parents:
diff changeset
584 to create it first. The path to the output folder can be either relative or absolute.
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parents:
diff changeset
585
62c6da72dd4a Uploaded
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parents:
diff changeset
586 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
62c6da72dd4a Uploaded
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parents:
diff changeset
587 the specified folder does not exist, Bismark will attempt to create it first. The path to the
62c6da72dd4a Uploaded
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parents:
diff changeset
588 temporary folder can be either relative or absolute.
62c6da72dd4a Uploaded
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parents:
diff changeset
589
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590 ------
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591
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parents:
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592 Bowtie 2 alignment options::
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parents:
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593
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parents:
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594 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
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parents:
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595 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
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parents:
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596 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
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parents:
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597 Bowtie 1 see -n).
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parents:
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598
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parents:
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599 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
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parents:
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600 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
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parents:
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601 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
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parents:
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602 Bowtie 1 see -l).
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parents:
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603
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parents:
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604 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
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parents:
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605 position to be the highest possible, regardless of the actual value. I.e. input is treated
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parents:
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606 as though all quality values are high. This is also the default behavior when the input
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parents:
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607 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
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parents:
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608
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parents:
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609
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parents:
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610 Bowtie 2 paired-end options::
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parents:
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611
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parents:
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612 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
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parents:
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613 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
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parents:
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614 and on by default.
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parents:
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615
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parents:
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616 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
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parents:
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617 A discordant alignment is an alignment where both mates align uniquely, but that does not
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618 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
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619 and it is on by default.
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parents:
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620
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621
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parents:
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622 Bowtie 2 effort options::
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parents:
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623
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624 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
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parents:
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625 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
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parents:
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626 new second-best alignment. Default: 15.
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parents:
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627
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parents:
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628 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
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parents:
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629 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
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parents:
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630 mismatches allowed) at different offsets and searches for more alignments. A read is considered
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parents:
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631 to have repetitive seeds if the total number of seed hits divided by the number of seeds
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parents:
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632 that aligned at least once is greater than 300. Default: 2.
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parents:
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633
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parents:
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634
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parents:
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635 Bowtie 2 Scoring options::
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parents:
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636
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parents:
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637 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
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parents:
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638 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
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639 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
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parents:
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640 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
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parents:
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641 L,0,-0.2.
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parents:
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642
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parents:
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643
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parents:
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644 Bowtie 2 Reporting options::
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parents:
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645
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parents:
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646 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
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parents:
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647 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
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parents:
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648 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
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parents:
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649 effort expended to find valid alignments.
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parents:
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650
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parents:
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651 For reference, this used to be the old (now deprecated) description of -M:
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parents:
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652 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
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parents:
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653 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
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parents:
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654 happens first. Only the best alignment is reported. Information from the other alignments is used to
4
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parents: 3
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655 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
0
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parents:
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656 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
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parents:
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657 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
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parents:
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658 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
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659 always used and its default value is set to 10.
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parents:
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660
4
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parents: 3
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661 ]]>
0
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parents:
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662 </help>
4
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parents: 3
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663 <citations>
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parents: 3
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664 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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parents: 3
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665 </citations>
0
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666 </tool>