annotate bismark_bowtie_wrapper.xml @ 4:243e8f9fb75b draft

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author bgruening
date Mon, 09 Feb 2015 18:24:41 -0500
parents 91f07ff056ca
children b100248c35b8
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1 <tool id="bismark_bowtie" name="Bismark" version="0.10.0">
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2 <!-- Wrapper compatible with Bismark version 0.10 -->
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3 <description>bisulfite mapper (bowtie)</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="0.12.8">bowtie</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 ##--bismark_path \$SCRIPT_PATH
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21
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22 ##
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23 ## Bismark Genome Preparation, if desired.
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24 ##
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25
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26 ## Handle reference file.
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27 #if $refGenomeSource.genomeSource == "history":
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28 --own-file=$refGenomeSource.ownFile
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29 #else:
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30 --indexes-path ${refGenomeSource.index.fields.path}
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31 #end if
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32
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33
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34 ##
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35 ## Input parameters
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36 ##
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37
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38
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39 #if $singlePaired.sPaired == "single":
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40 --single-paired $singlePaired.input_singles
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41
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42 #if $singlePaired.input_singles.ext == "fastqillumina":
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43 --phred64-quals
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44 --fastq
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45 #elif $singlePaired.input_singles.ext == "fastqsanger":
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46 --fastq
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47 #elif $singlePaired.input_singles.ext == "fasta":
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48 --fasta
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49 #end if
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50 #else:
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51 --mate-paired
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52 #set $mate1 = list()
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53 #set $mate2 = list()
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54 #for $mate_pair in $singlePaired.mate_list
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55 $mate1.append( str($mate_pair.input_mate1) )
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56 $mate2.append( str($mate_pair.input_mate2) )
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57 #end for
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58
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59 --mate1 #echo ','.join($mate1)
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60 --mate2 #echo ','.join($mate2)
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61
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62 #for $mate_pair in $singlePaired.mate_list:
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63 #if $mate_pair.input_mate1.ext == "fastqillumina":
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64 --phred64-quals
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65 --fastq
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66 #elif $mate_pair.input_mate1.ext == "fastqsanger":
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67 --fastq
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68 #elif $mate_pair.input_mate1.ext == "fasta":
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69 --fasta
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70 #end if
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71 #break
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72 #end for
0
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73
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74 -I $singlePaired.minInsert
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75 -X $singlePaired.maxInsert
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76 #end if
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77
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78
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79 ## for now hardcode the value for the required memory per thread in --best mode
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80 --chunkmbs 512
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81
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82
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83 #if $params.settingsType == "custom":
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84
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85 ## default 20
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86 --seed-len $params.seed_len
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87 ## default 0
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88 --seed-mismatches $params.seed_mismatches
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89
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90 ## default 70
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91 ##--maqerr $params.maqerr
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92
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93 ## default unlimited
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94 #if $params.qupto != 0:
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95 --qupto $params.qupto
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96 #end if
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97 #if $params.skip_reads != 0:
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98 --skip-reads $params.skip_reads
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99 #end if
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100
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101 #if $params.bismark_stdout:
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102 --stdout $output_stdout
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103 #end if
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104
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105 #if $params.isReportOutput:
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106 --output-report-file $report_file
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107 #end if
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108
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109 #end if
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110
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111 ##
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112 ## Output parameters.
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113 ##
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114 --output $output
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115 ##$suppress_header
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116
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117 #if str( $singlePaired.sPaired ) == "single"
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118 #if $output_unmapped_reads_l
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119 --output-unmapped-reads $output_unmapped_reads_l
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120 #end if
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121 #if $output_suppressed_reads_l
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122 --output-suppressed-reads $output_suppressed_reads_l
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123 #end if
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124 #else
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125 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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126 --output-unmapped-reads-l $output_unmapped_reads_l
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127 --output-unmapped-reads-r $output_unmapped_reads_r
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128 #end if
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129 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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130 --output-suppressed-reads-l $output_suppressed_reads_l
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131 --output-suppressed-reads-r $output_suppressed_reads_r
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132 #end if
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133 #end if
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134
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135 ]]>
0
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136 </command>
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137 <inputs>
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138 <conditional name="refGenomeSource">
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139 <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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140 <option value="indexed">Use a built-in index</option>
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141 <option value="history">Use one from the history</option>
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142 </param>
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143 <when value="indexed">
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144 <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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145 <options from_data_table="bowtie_indexes">
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146 <filter type="sort_by" column="2"/>
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147 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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148 </options>
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149 </param>
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150 </when> <!-- build-in -->
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151 <when value="history">
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152 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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153 </when> <!-- history -->
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154 </conditional> <!-- refGenomeSource -->
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155
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156 <!-- Input Parameters -->
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157 <conditional name="singlePaired">
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158 <param name="sPaired" type="select" label="Is this library mate-paired?">
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159 <option value="single">Single-end</option>
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160 <option value="paired">Paired-end</option>
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161 </param>
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162 <when value="single">
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163 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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164 </when>
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165 <when value="paired">
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166 <repeat name="mate_list" title="Paired End Pairs" min="1">
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167 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
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168 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
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169 </repeat>
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170 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
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171 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
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172 </when>
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173 </conditional>
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174
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175
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176 <conditional name="params">
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177 <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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178 <option value="default">Use Defaults</option>
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179 <option value="custom">Full parameter list</option>
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180 </param>
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181 <when value="default" />
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182 <!-- Full/advanced params. -->
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183 <when value="custom">
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184 <!-- -n -->
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185 <param name="seed_mismatches" type="select" label="The maximum number of mismatches permitted in the 'seed'">
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186 <option value="0">0</option>
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parents:
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187 <option value="1">1</option>
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188 <option value="2" selected="true">2</option>
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189 <option value="3">3</option>
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190 </param>
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191 <!-- -l -->
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192 <param name="seed_len" type="integer" value="28" label="The 'seed length'; The number of bases of the high quality end of the read to which the maximum number of mismatches applies" />
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193 <!--
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194 <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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195 -->
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196 <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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197 <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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198
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199 <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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200 <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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201 <!-- output Options -->
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202 <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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203 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
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204 <!--end output options -->
0
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205 </when> <!-- full -->
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206 </conditional> <!-- params -->
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207 <!--
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208 <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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209 -->
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210 </inputs>
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211 <outputs>
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212 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
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213 <filter>
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214 ((
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215 params['settingsType'] == "custom" and
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216 params['isReportOutput'] is True
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217 ))
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218 </filter>
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219 </data>
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220 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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221 <filter>
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222 ((
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223 params['settingsType'] == "custom" and
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224 params['bismark_stdout'] is True
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225 ))
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226 </filter>
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227 </data>
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228
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229 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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230 <actions>
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231 <conditional name="refGenomeSource.genomeSource">
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232 <when value="indexed">
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233 <action type="metadata" name="dbkey">
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234 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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235 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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236 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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237 </option>
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238 </action>
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239 </when>
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240 <when value="history">
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241 <action type="metadata" name="dbkey">
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242 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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243 </action>
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244 </when>
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245 </conditional>
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246 </actions>
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247 </data>
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248
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249 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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250 <filter>
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251 ((
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252 params['settingsType'] == "custom" and
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253 params['suppressed_read_file'] is True
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254 ))
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255 </filter>
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256 <actions>
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257 <conditional name="singlePaired.sPaired">
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258 <when value="single">
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259 <action type="format">
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260 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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261 </action>
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262 </when>
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263 <when value="paired">
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264 <!--action type="format">
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265 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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266 </action-->
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267 </when>
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268 </conditional>
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269 </actions>
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270 </data>
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271
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272 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
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273 <filter>singlePaired['sPaired'] == "paired"</filter>
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274 <filter>params['settingsType'] == "custom"</filter>
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275 <filter>params['supressed_read_file'] is True</filter>
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276 <actions>
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277 <conditional name="singlePaired.sPaired">
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278 <when value="single">
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279 <action type="format">
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280 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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281 </action>
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282 </when>
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283 <when value="paired">
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284 <!--action type="format">
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285 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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286 </action-->
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287 </when>
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288 </conditional>
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289 </actions>
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290 </data>
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291
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292 <!-- Outout unmapped reads -->
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293 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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294 <filter>
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295 ((
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296 params['settingsType'] == "custom" and
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297 params['unmapped_read_file'] is True
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298 ))
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299 </filter>
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300 <actions>
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301 <conditional name="singlePaired.sPaired">
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302 <when value="single">
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303 <action type="format">
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304 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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305 </action>
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306 </when>
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307 <when value="paired">
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308 <!--action type="format">
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309 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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310 </action-->
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311 </when>
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312 </conditional>
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313 </actions>
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314 </data>
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315 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
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316 <filter>singlePaired['sPaired'] == "paired"</filter>
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317 <filter>params['settingsType'] == "custom"</filter>
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318 <filter>params['unmapped_read_file'] is True</filter>
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319 <actions>
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320 <conditional name="singlePaired.sPaired">
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321 <when value="single">
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322 <action type="format">
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323 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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324 </action>
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325 </when>
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326 <when value="paired">
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327 <!--action type="format">
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328 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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329 </action-->
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330 </when>
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331 </conditional>
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332 </actions>
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333 </data>
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334 </outputs>
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335
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336 <tests>
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337 </tests>
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338
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339 <help>
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340 <![CDATA[
0
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341
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parents:
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342 **What it does**
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343
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344 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
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345 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
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346 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
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347 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
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348 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
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349 forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
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350 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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351 sequence from the genome and determine if there were any protected C's present or not.
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352
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parents:
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353 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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354
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355 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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356 re-enabled by using non_directional mode.
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357
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358 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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359
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parents:
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360 ------
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361
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362 **Know what you are doing**
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363
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364 .. class:: warningmark
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365
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366 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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367
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368 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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369
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370
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371 .. class:: warningmark
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372
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373 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:
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374
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parents:
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375 ------
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376
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377 **Input formats**
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378
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379 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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380
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381 ------
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382
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383 **A Note on Built-in Reference Genomes**
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384
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385 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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386
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387 ------
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388
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389 The final output of Bismark is in SAM format by default.
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390
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parents:
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391 **Outputs**
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392
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393 The output is in SAM format, and has the following columns::
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394
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395 Column Description
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396 -------- --------------------------------------------------------
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397 1 QNAME seq-ID
4
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398 2 FLAG this flag tries to take the strand a bisulfite read
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399 originated from into account
0
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400 (this is different from ordinary DNA alignment flags!)
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parents:
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401 3 RNAME chromosome
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parents:
diff changeset
402 4 POS start position
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parents:
diff changeset
403 5 MAPQ always 255
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parents:
diff changeset
404 6 CIGAR extended CIGAR string
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parents:
diff changeset
405 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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parents:
diff changeset
406 8 MPOS 1-based Mate POSition
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parents:
diff changeset
407 9 ISIZE Inferred insert SIZE
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parents:
diff changeset
408 10 SEQ query SEQuence on the same strand as the reference
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parents:
diff changeset
409 11 QUAL Phred33 scale
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parents:
diff changeset
410 12 NM-tag edit distance to the reference)
4
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parents: 3
diff changeset
411 13 XX-tag base-by-base mismatches to the reference.
0
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parents:
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412 This does not include indels.
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parents:
diff changeset
413 14 XM-tag methylation call string
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parents:
diff changeset
414 15 XR-tag read conversion state for the alignment
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parents:
diff changeset
415 16 XG-tag genome conversion state for the alignment
4
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parents: 3
diff changeset
416
0
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parents:
diff changeset
417
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parents:
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418 Each read of paired-end alignments is written out in a separate line in the above format.
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parents:
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419
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parents:
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420
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parents:
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421 It looks like this (scroll sideways to see the entire example)::
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parents:
diff changeset
422
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parents:
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423 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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parents:
diff changeset
424 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:
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425 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
426
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parents:
diff changeset
427 -------
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parents:
diff changeset
428
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parents:
diff changeset
429 **Bismark settings**
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parents:
diff changeset
430
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parents:
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431 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
432
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parents:
diff changeset
433 ------
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parents:
diff changeset
434
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parents:
diff changeset
435 **Bismark parameter list**
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parents:
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436
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parents:
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437 This is an exhaustive list of Bismark options.
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parents:
diff changeset
438
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parents:
diff changeset
439 Input::
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parents:
diff changeset
440
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parents:
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441 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
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parents:
diff changeset
442 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
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parents:
diff changeset
443 produce one mapping result and one report file per input file.
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parents:
diff changeset
444
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parents:
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445 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
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parents:
diff changeset
446 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
447 correspond file-for-file and read-for-read with those specified in mates2.
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parents:
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448 Reads may be a mix of different lengths. Bismark will produce one mapping result
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parents:
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449 and one report file per paired-end input file pair.
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parents:
diff changeset
450
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parents:
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451 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
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parents:
diff changeset
452 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
453 correspond file-for-file and read-for-read with those specified in mates1.
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parents:
diff changeset
454 Reads may be a mix of different lengths.
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parents:
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455
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parents:
diff changeset
456 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
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parents:
diff changeset
457 files (usually having extension .fg or .fastq). This is the default. See also
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parents:
diff changeset
458 --solexa-quals.
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parents:
diff changeset
459
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parents:
diff changeset
460 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
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parents:
diff changeset
461 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
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parents:
diff changeset
462 are assumed to be 40 on the Phred scale.
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parents:
diff changeset
463
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parents:
diff changeset
464 -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
465
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parents:
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466 -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
467
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parents:
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468 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
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parents:
diff changeset
469
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parents:
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470 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
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parents:
diff changeset
471
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parents:
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472 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
4
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parents: 3
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473 (which can't). The formula for conversion is:
0
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parents:
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474 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
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parents:
diff changeset
475 is usually the right option for use with (unconverted) reads emitted by the GA
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parents:
diff changeset
476 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
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parents:
diff changeset
477
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parents:
diff changeset
478 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
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parents:
diff changeset
479 reads emitted by GA Pipeline version 1.3 or later. Default: off.
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parents:
diff changeset
480
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parents:
diff changeset
481
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parents:
diff changeset
482 Alignment::
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parents:
diff changeset
483
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parents:
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484 -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
485 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
486 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
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parents:
diff changeset
487
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parents:
diff changeset
488 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
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parents:
diff changeset
489 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
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parents:
diff changeset
490 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
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parents:
diff changeset
491
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parents:
diff changeset
492 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
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parents:
diff changeset
493 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
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parents:
diff changeset
494 quality values to the nearest 10 and saturates at 30. This value is not relevant for
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parents:
diff changeset
495 Bowtie 2.
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parents:
diff changeset
496
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parents:
diff changeset
497 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
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parents:
diff changeset
498 --best mode. Best-first search must keep track of many paths at once to ensure it is
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parents:
diff changeset
499 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
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parents:
diff changeset
500 memory impact of the descriptors, but they can still grow very large in some cases. If
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parents:
diff changeset
501 you receive an error message saying that chunk memory has been exhausted in --best mode,
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parents:
diff changeset
502 try adjusting this parameter up to dedicate more memory to the descriptors. This value
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parents:
diff changeset
503 is not relevant for Bowtie 2. Default: 512.
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parents:
diff changeset
504
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parents:
diff changeset
505 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
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parents:
diff changeset
506 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
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parents:
diff changeset
507 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
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parents:
diff changeset
508 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
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parents:
diff changeset
509
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parents:
diff changeset
510 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
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parents:
diff changeset
511 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
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parents:
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512 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
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parents:
diff changeset
513 A 61-bp gap would not be valid in that case. Default: 500.
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parents:
diff changeset
514
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parents:
diff changeset
515
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parents:
diff changeset
516
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parents:
diff changeset
517 Output::
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parents:
diff changeset
518
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parents:
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519 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
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parents:
diff changeset
520 bisulfite strands will be reported. Default: OFF.
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parents:
diff changeset
521
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parents:
diff changeset
522 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
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parents:
diff changeset
523 to the original strands are merely theoretical and should not exist in reality. Specifying directional
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parents:
diff changeset
524 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
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parents:
diff changeset
525 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
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parents:
diff changeset
526 for sprand-specific libraries).
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parents:
diff changeset
527
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parents:
diff changeset
528 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
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parents:
diff changeset
529 split up into several smaller files to run concurrently and the output files are to be merged.
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parents:
diff changeset
530
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parents:
diff changeset
531 --quiet Print nothing besides alignments.
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parents:
diff changeset
532
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parents:
diff changeset
533 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
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parents:
diff changeset
534 of SAM format output.
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parents:
diff changeset
535
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parents:
diff changeset
536 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
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parents:
diff changeset
537 appear as they did in the input, without any translation of quality values that may have
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parents:
diff changeset
538 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
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parents:
diff changeset
539 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
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parents:
diff changeset
540 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
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parents:
diff changeset
541 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
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parents:
diff changeset
542
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parents:
diff changeset
543 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
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parents:
diff changeset
544 mismatches or other reads that fail to align uniquely to a file in the output directory.
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parents:
diff changeset
545 Written reads will appear as they did in the input, without any of the translation of quality
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parents:
diff changeset
546 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
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parents:
diff changeset
547 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
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parents:
diff changeset
548 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
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parents:
diff changeset
549
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parents:
diff changeset
550 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
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parents:
diff changeset
551 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
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parents:
diff changeset
552 to create it first. The path to the output folder can be either relative or absolute.
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parents:
diff changeset
553
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parents:
diff changeset
554 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
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parents:
diff changeset
555 the specified folder does not exist, Bismark will attempt to create it first. The path to the
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parents:
diff changeset
556 temporary folder can be either relative or absolute.
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parents:
diff changeset
557
4
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parents: 3
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558 ]]>
0
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parents:
diff changeset
559 </help>
4
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parents: 3
diff changeset
560 <citations>
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parents: 3
diff changeset
561 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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parents: 3
diff changeset
562 </citations>
0
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parents:
diff changeset
563 </tool>