Mercurial > repos > bgruening > bismark

annotate bismark_bowtie2_wrapper.xml @ 25:a5faad9e4138 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author bgruening
date Wed, 22 Aug 2018 08:09:23 -0400
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25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0" profile="18.01">
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2 <description>Bisulfite reads mapper</description>
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3 <requirements>
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4 <requirement type="package" version="0.20.0">bismark</requirement>
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5 <requirement type="package" version="1.8">samtools</requirement>
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6 <requirement type="package" version="2.3.4.2">bowtie2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 python '$__tool_directory__/bismark_wrapper.py'
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10
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11 ## Change this to accommodate the number of threads you have available.
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12 --num-threads "\${GALAXY_SLOTS:-4}"
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13
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14 ##
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15 ## Bismark Genome Preparation, if desired.
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16 ##
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17
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18 ## Handle reference file.
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19 #if $refGenomeSource.genomeSource == "built_in_fasta":
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20 --own-file '${refGenomeSource.built_in_fasta.fields.path}'
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21 #else if $refGenomeSource.genomeSource == "history":
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22 --own-file '$refGenomeSource["own_file"]'
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23 #else:
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24 --indexes-path '${refGenomeSource.built_in_indexes.fields.path}'
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25 #end if
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26
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27 ##
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28 ## Input parameters
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29 ##
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30
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31 #if $singlePaired.sPaired == "single":
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32 --single-paired '$singlePaired.input_singles'
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33
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34 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]:
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35 --phred64-quals
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36 --fastq
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37 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]:
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38 --fastq
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39 #elif $singlePaired.input_singles.ext == "fasta":
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40 --fasta
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41 #end if
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42 #else:
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43 --mate-paired
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44 #set $mate1 = list()
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45 #set $mate2 = list()
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46 #for $mate_pair in $singlePaired.mate_list
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47 $mate1.append( str($mate_pair.input_mate1) )
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48 $mate2.append( str($mate_pair.input_mate2) )
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49 #end for
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50
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51 --mate1 #echo ','.join($mate1)
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52 --mate2 #echo ','.join($mate2)
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53
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54 #for $mate_pair in $singlePaired.mate_list:
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55 #if $mate_pair.input_mate1.ext == "fastqillumina":
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56 --phred64-quals
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57 --fastq
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58 #elif $mate_pair.input_mate1.ext in "fastqsanger,fastqsanger.gz":
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59 --fastq
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60 #elif $mate_pair.input_mate1.ext == "fasta":
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61 --fasta
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62 #end if
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63 #break
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64 #end for
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65
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66 -I $singlePaired.minInsert
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67 -X $singlePaired.maxInsert
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68 #end if
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69
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70 #if $sort_bam:
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71 --sort-bam
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72 #end if
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73
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74 ## for now hardcode the value for the required memory per thread in --best mode
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75 --chunkmbs 512
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76
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77
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78 #if $params.settingsType == "custom":
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79
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80 ## default 20
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81 --seed-len $params.seed_len
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82 ## default 0
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83 --seed-mismatches $params.seed_mismatches
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84 ## default 15
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85 --seed-extention-attempts $params.seed_extention_attempts
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86 ## default 2
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87 --max-reseed $params.max_reseed
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88
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89 ## default 70
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90 ##--maqerr $params.maqerr
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91
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92 ## default unlimited
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93 #if $params.qupto != 0:
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94 --qupto $params.qupto
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95 #end if
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96 #if $params.skip_reads != 0:
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97 --skip-reads $params.skip_reads
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98 #end if
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99
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100 ## if set, disable the original behaviour
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101 $params.no_mixed
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102 ## if set, disable the original behaviour
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103 $params.no_discordant
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104
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105 #if $params.bismark_stdout:
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106 --stdout '$output_stdout'
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107 #end if
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108
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109 #if $params.isReportOutput:
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110 --output-report-file '$report_file'
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111 #end if
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112
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113 #else:
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114 --output-report-file '$report_file'
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115 #end if
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116
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117 ##
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118 ## Output parameters.
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119 ##
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120 --output '$output'
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121 ##$suppress_header
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122
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123 #if str( $singlePaired.sPaired ) == "single"
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124 #if $output_unmapped_reads_l
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125 --output-unmapped-reads '$output_unmapped_reads_l'
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126 #end if
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127 #if $output_suppressed_reads_l
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128 --output-suppressed-reads '$output_suppressed_reads_l'
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129 #end if
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130 #else
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131 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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132 --output-unmapped-reads-l '$output_unmapped_reads_l'
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133 --output-unmapped-reads-r '$output_unmapped_reads_r'
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134 #end if
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135 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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136 --output-suppressed-reads-l '$output_suppressed_reads_l'
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137 --output-suppressed-reads-r '$output_suppressed_reads_r'
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138 #end if
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139 #end if
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140
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141 ]]>
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142 </command>
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143 <inputs>
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144 <conditional name="refGenomeSource">
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145 <param name="genomeSource" type="select"
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146 label="Will you select a reference genome from your history or use a built-in index?"
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147 help="Built-ins were indexed using default options">
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148 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
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149 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
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150 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
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151 </param>
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152 <when value="built_in_indexes">
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153 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)"
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154 help="If your genome of interest is not listed, contact your Galaxy admin">
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155 <options from_data_table="bismark_indexes">
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156 <filter type="sort_by" column="name"/>
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157 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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158 </options>
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159 </param>
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160 </when>
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161 <when value="built_in_fasta">
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162 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
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163 <options from_data_table="all_fasta">
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164 <filter type="sort_by" column="name"/>
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165 <validator type="no_options"
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166 message="No genomes in fasta are available for the selected input dataset"/>
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167 </options>
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168 </param>
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169 </when>
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170 <when value="history">
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171 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
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172 </when>
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173 </conditional>
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174
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175 <!-- Input Parameters -->
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176 <conditional name="singlePaired">
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177 <param name="sPaired" type="select" label="Is this library mate-paired?">
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178 <option value="single">Single-end</option>
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179 <option value="paired">Paired-end</option>
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180 </param>
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181 <when value="single">
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182 <param name="input_singles" type="data"
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183 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file"
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184 help="FASTQ or FASTA files."/>
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185 </when>
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186 <when value="paired">
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187 <repeat name="mate_list" title="Paired End Pairs" min="1">
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188 <param name="input_mate1" type="data"
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189 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1"
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190 help="FASTQ or FASTA files."/>
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191 <param name="input_mate2" type="data"
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192 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2"
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193 help="FASTQ or FASTA files."/>
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194 </repeat>
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195 <param name="minInsert" type="integer" value="0"
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196 label="Minimum insert size for valid paired-end alignments"/>
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197 <param name="maxInsert" type="integer" value="500"
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198 label="Maximum insert size for valid paired-end alignments"/>
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199 </when>
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200 </conditional>
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201
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202 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False"
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203 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
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204
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205 <conditional name="params">
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206 <param name="settingsType" type="select" label="Bismark settings to use"
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207 help="You can use the default settings or set custom values for any of Bismark's parameters.">
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208 <option value="default">Use Defaults</option>
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209 <option value="custom">Full parameter list</option>
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210 </param>
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211 <!-- Full/advanced params. -->
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212 <when value="dafault"></when>
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213 <when value="custom">
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214 <!-- -N -->
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215 <param name="seed_mismatches" type="integer" value="0"
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216 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
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217 <!-- -L -->
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218 <param name="seed_len" type="integer" value="20"
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219 label="Length of the seed substrings to align during multiseed alignment"/>
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220 <!--
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221 <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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222 -->
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223 <!-- -D -->
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224 <param name="seed_extention_attempts" type="integer" value="15"
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225 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
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226 <!-- -R -->
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227 <param name="max_reseed" type="integer" value="2"
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228 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/>
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229
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230 <param name="qupto" type="integer" value="0"
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231 label="Only aligns the first N reads or read pairs from the input"
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232 help="Default is 0 and means 'no-limit'."/>
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233 <param name="skip_reads" type="integer" value="0"
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234 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
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235
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236 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
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237 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
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238 help=""/>
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239 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
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240 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads"
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241 help=""/>
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242
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243 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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244 label="Write ambiguous reads to an extra output file"
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245 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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246 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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247 label="Write all reads that could not be aligned to a file"/>
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248 <!-- output Options -->
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249 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
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250 label="Write the bismark output and summary information to an extra file"/>
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251 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
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252 label="Offer all report files concatenated in one file (Mapping Report)"/>
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253
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254 <!--end output options -->
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255 </when> <!-- full -->
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256 </conditional> <!-- params -->
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257 <!--
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258 <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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259 -->
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260 </inputs>
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261
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262
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263 <outputs>
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264 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
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265 <filter>
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266 ((
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267 params['settingsType'] == "default" or
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268 ( params['settingsType'] == "custom" and
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269 params['isReportOutput'] is True )
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270 ))
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271 </filter>
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272 </data>
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273 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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274 <filter>
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275 ((
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276 params['settingsType'] == "custom" and
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277 params['bismark_stdout'] is True
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278 ))
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279 </filter>
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280 </data>
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281
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282 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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283 <actions>
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284 <conditional name="refGenomeSource.genomeSource">
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285 <when value="built_in_indexes">
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286 <action type="metadata" name="dbkey">
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287 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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288 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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289 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
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290 </option>
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291 </action>
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292 </when>
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293 <when value="generate_indexes">
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294 <action type="metadata" name="dbkey">
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295 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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296 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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297 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
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298 </option>
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299 </action>
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300 </when>
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301 </conditional>
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302 </actions>
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303 <change_format>
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304 <when input="sort_bam" value="true" format="bam"/>
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305 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/>
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306 </change_format>
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307 </data>
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308
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309 <data format="fastq" name="output_suppressed_reads_l"
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310 label="${tool.name} on ${on_string}: suppressed reads (L)">
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311 <filter>
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312 ((
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313 params['settingsType'] == "custom" and
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314 params['suppressed_read_file'] is True
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315 ))
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316 </filter>
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317 <actions>
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318 <conditional name="singlePaired.sPaired">
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319 <when value="single">
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320 <action type="format">
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321 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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322 </action>
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323 </when>
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324 </conditional>
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325 </actions>
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326 </data>
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327
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328 <data format="fastq" name="output_suppressed_reads_r"
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329 label="${tool.name} on ${on_string}: suppressed reads (R)">
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330 <filter>
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331 ((
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332 singlePaired['sPaired'] == "paired" and
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333 params['settingsType'] == "custom" and
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334 params['suppressed_read_file'] is True
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335 ))
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336 </filter>
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337 <actions>
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338 <conditional name="singlePaired.sPaired">
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339 <when value="single">
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340 <action type="format">
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341 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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342 </action>
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343 </when>
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344 <!--when value="paired">
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345 <action type="format">
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346 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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347 </action>
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348 </when-->
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349 </conditional>
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350 </actions>
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351 </data>
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352
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353 <!-- Outout unmapped reads -->
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354 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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355 <filter>
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356 ((
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357 params['settingsType'] == "custom" and
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358 params['unmapped_read_file'] is True
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359 ))
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360 </filter>
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361 <actions>
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362 <conditional name="singlePaired.sPaired">
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363 <when value="single">
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364 <action type="format">
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365 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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366 </action>
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367 </when>
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368 <!--when value="paired">
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369 <action type="format">
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370 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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371 </action>
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372 </when-->
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373 </conditional>
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374 </actions>
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375 </data>
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376 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
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377 <filter>
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378 ((
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379 singlePaired['sPaired'] == "paired" and
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380 params['settingsType'] == "custom" and
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381 params['unmapped_read_file'] is True
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382 ))
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383 </filter>
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384 <actions>
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385 <conditional name="singlePaired.sPaired">
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386 <when value="single">
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387 <action type="format">
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388 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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389 </action>
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390 </when>
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391 <!--when value="paired">
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392 <action type="format">
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393 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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394 </action>
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395 </when-->
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396 </conditional>
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397 </actions>
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398 </data>
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399 </outputs>
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400 <tests>
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401 <test>
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402 <param name="genomeSource" value="history"/>
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403 <param name="own_file" value="mm10.tiny.fa.gz" />
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404 <param name="sPaired" value="single"/>
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405 <param name="input_singles" value="input1.fq.gz" ftype="fastqsanger"/>
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406 <param name="sort_bam" value="false"/>
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407 <param name="settingsType" value="custom"/>
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408 <param name="suppressed_read_file" value="true"/>
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409 <param name="unmapped_read_file" value="true"/>
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410 <param name="bismark_stdout" value="true"/>
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411 <param name="isReportOutput" value="true"/>
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412
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413 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80">
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414 <assert_contents>
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415 <has_text text="Sequences analysed in total:" />
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416 <has_text text="44115" />
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417 <has_text text="Mapping efficiency:" />
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418 <has_text text="1.3%" />
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419 <has_text text="Bismark run complete" />
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420 </assert_contents>
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421 </output>
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422 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
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423 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
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424 </test>
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425 </tests>
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426
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427 <help>
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428 <![CDATA[
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429
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430 **What it does**
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431
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432 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome.
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433 | Sequence reads are transformed into a bisulfite converted forward strand version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
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434 | Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the forward strand, by doing this alignments will produce the same positions).
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435 | These instances of Bowtie 2 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original sequence from the genome and determine if there were any protected C's present or not.
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436 |
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437 | 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 re-enabled by using non_directional mode.
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438 |
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439 | 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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440
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441 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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442
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443 ----
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444
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445 **Know what you are doing**
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446
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447 .. class:: warningmark
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448
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449 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco.
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450 | In other words = running this tool with default parameters will probably not give you meaningful results.
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451 | 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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452 |
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453
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454 .. class:: warningmark
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455
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456 | 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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457
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458 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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459
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460 ----
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461
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462 **Input formats**
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463
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464 | 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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465
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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466 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
467
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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468 **A Note on Built-in Reference Genomes**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
469
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
470 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
471 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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472 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
473
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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474 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
475
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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476 **Outputs**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
477
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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478 * The final output of Bismark is in SAM format by default, and has the following columns::
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
479
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
480 Column Description
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
481 -------- --------------------------------------------------------
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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482 1 QNAME seq-ID
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
483 2 FLAG this flag tries to take the strand a bisulfite read
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
484 originated from into account
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
485 (this is different from ordinary DNA alignment flags!)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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486 3 RNAME chromosome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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487 4 POS start position
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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488 5 MAPQ always 255
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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489 6 CIGAR extended CIGAR string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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490 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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491 8 MPOS 1-based Mate POSition
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
492 9 ISIZE Inferred insert SIZE
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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493 10 SEQ query SEQuence on the same strand as the reference
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
494 11 QUAL Phred33 scale
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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495 12 NM-tag edit distance to the reference)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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496 13 XX-tag base-by-base mismatches to the reference.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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497 This does not include indels.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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498 14 XM-tag methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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499 15 XR-tag read conversion state for the alignment
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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500 16 XG-tag genome conversion state for the alignment
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
501
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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502
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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503 | Each read of paired-end alignments is written out in a separate line in the above format.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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504 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
505
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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506 * It looks like this (scroll sideways to see the entire example)::
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
507
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
508 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
509 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
510 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
511
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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512 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
513
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
514 **Note on Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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515
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
516 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
517
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
518 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
519
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
520 **Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
521
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
522 * **If Paired-End Reads**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
523
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
524 * **Minimum insert size for valid paired-end alignments**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
525
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
526 | The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. Default: 0.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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527 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
528 | Alignment option *-I/--minins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
529
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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530
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
531 * **Maximum insert size for valid paired-end alignments**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
532
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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533 | The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. Default: 500.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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534 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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535 | Alignment option *-X/--maxins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
536
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
537
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
538 * **Number of mismatches to be allowed in a seed alignment during multiseed alignment**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
539
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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540 | Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for Bowtie 1 see -n).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
541 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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542 | Bowtie 2 Specific option *-N <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
543
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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544 * **Length of the seed substrings to align during multiseed alignment**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
545
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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546 | Sets the length of the seed substrings to align during multiseed alignment. Smaller values make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is used by default, which sets -L to 20. This option is only available for Bowtie 2 (for Bowtie 1 see -l).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
547 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
548 | Bowtie 2 Specific option *-L <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
549
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
550
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
551 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
552
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
553 | Up to <int> consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using the alignments found so far. A seed extension "fails" if it does not yield a new best or a new second-best alignment. Default: 15.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
554 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
555 | Bowtie 2 Effort option *-D <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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556
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557 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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558
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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559 | <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default: 2.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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560 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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561 | Bowtie 2 Effort option *-R <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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562
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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563 * **Only aligns the first N reads or read pairs from the input**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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564
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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565 | Only aligns the first <int> reads or read pairs from the input. Default: no limit.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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566 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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567 | Input option *-u/--upto <INT>*
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568
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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569 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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570
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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571 | Input option *-s/--skip*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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572
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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573 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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574
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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575 | Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior and it is on by default.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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576 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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577 | Bowtie 2 Paired-End option *--no-discordant*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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578
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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579 * **Disable Bowtie 2's behaviour to try to find alignments for the individual mates**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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580
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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581 | This option disables Bowtie 2's behavior to try to find alignments for the individual mates if it cannot find a concordant or discordant alignment for a pair. This option is invariable and on by default.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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582 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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583 | Bowtie 2 Paired-End option *--no-mixed*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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584
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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585 * **Write ambiguous reads to an extra output file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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586
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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587 | 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 to a file in the output directory. Written reads will appear as they did in the input, without any of the translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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588 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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589 | Output option *--ambiguous*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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590
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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591 * **Write all reads that could not be aligned to a file**
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592
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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593 | Write all reads that could not be aligned to a file in the output directory. Written reads will appear as they did in the input, without any translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping) are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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594 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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595 | Output option *-un/--unmapped*
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596
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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597 * **Offer all report files concatenated in one file**
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598
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599 | Prints out a Bismark mapping report
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600
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601 ]]>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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602 </help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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603 <citations>
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604 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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605 </citations>
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606 </tool>