Mercurial > repos > bgruening > bismark

annotate bismark_bowtie2_wrapper.xml @ 27:b26a0df246fd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b
author bgruening
date Tue, 26 Feb 2019 18:41:44 -0500
parents cbfd9b10eff6
children 4e274666de78
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b26a0df246fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.2" 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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14 ##
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15 ## Bismark Genome Preparation, if desired.
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16 ##
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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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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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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
26
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105 $params.non_directional
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106
25
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107 #if $params.bismark_stdout:
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108 --stdout '$output_stdout'
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109 #end if
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110
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111 #if $params.isReportOutput:
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112 --output-report-file '$report_file'
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113 #end if
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114
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115 #else:
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116 --output-report-file '$report_file'
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117 #end if
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118
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119 ##
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120 ## Output parameters.
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121 ##
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122 --output '$output'
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123 ##$suppress_header
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124
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125 #if str( $singlePaired.sPaired ) == "single"
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126 #if $output_unmapped_reads_l
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127 --output-unmapped-reads '$output_unmapped_reads_l'
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128 #end if
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129 #if $output_suppressed_reads_l
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130 --output-suppressed-reads '$output_suppressed_reads_l'
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131 #end if
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132 #else
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133 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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134 --output-unmapped-reads-l '$output_unmapped_reads_l'
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135 --output-unmapped-reads-r '$output_unmapped_reads_r'
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136 #end if
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137 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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138 --output-suppressed-reads-l '$output_suppressed_reads_l'
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139 --output-suppressed-reads-r '$output_suppressed_reads_r'
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140 #end if
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141 #end if
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142
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143 ]]>
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144 </command>
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145 <inputs>
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146 <conditional name="refGenomeSource">
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147 <param name="genomeSource" type="select"
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148 label="Will you select a reference genome from your history or use a built-in index?"
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149 help="Built-ins were indexed using default options">
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150 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
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151 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
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152 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
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153 </param>
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154 <when value="built_in_indexes">
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155 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)"
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156 help="If your genome of interest is not listed, contact your Galaxy admin">
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157 <options from_data_table="bismark_indexes">
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158 <filter type="sort_by" column="name"/>
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159 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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160 </options>
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161 </param>
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162 </when>
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163 <when value="built_in_fasta">
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164 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
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165 <options from_data_table="all_fasta">
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166 <filter type="sort_by" column="name"/>
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167 <validator type="no_options"
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168 message="No genomes in fasta are available for the selected input dataset"/>
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169 </options>
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170 </param>
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171 </when>
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172 <when value="history">
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173 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
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174 </when>
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175 </conditional>
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176
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177 <!-- Input Parameters -->
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178 <conditional name="singlePaired">
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179 <param name="sPaired" type="select" label="Is this library mate-paired?">
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180 <option value="single">Single-end</option>
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181 <option value="paired">Paired-end</option>
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182 </param>
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183 <when value="single">
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184 <param name="input_singles" type="data"
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185 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file"
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186 help="FASTQ or FASTA files."/>
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187 </when>
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188 <when value="paired">
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189 <repeat name="mate_list" title="Paired End Pairs" min="1">
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190 <param name="input_mate1" type="data"
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191 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1"
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192 help="FASTQ or FASTA files."/>
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193 <param name="input_mate2" type="data"
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194 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2"
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195 help="FASTQ or FASTA files."/>
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196 </repeat>
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197 <param name="minInsert" type="integer" value="0"
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198 label="Minimum insert size for valid paired-end alignments"/>
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199 <param name="maxInsert" type="integer" value="500"
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200 label="Maximum insert size for valid paired-end alignments"/>
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201 </when>
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202 </conditional>
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203
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204 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False"
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205 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
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206
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207 <conditional name="params">
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208 <param name="settingsType" type="select" label="Bismark settings to use"
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209 help="You can use the default settings or set custom values for any of Bismark's parameters.">
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210 <option value="default">Use Defaults</option>
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211 <option value="custom">Full parameter list</option>
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212 </param>
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213 <!-- Full/advanced params. -->
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214 <when value="dafault"></when>
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215 <when value="custom">
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216 <!-- -N -->
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217 <param name="seed_mismatches" type="integer" value="0"
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218 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
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219 <!-- -L -->
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220 <param name="seed_len" type="integer" value="20"
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221 label="Length of the seed substrings to align during multiseed alignment"/>
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222 <!--
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223 <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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224 -->
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225 <!-- -D -->
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226 <param name="seed_extention_attempts" type="integer" value="15"
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227 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
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228 <!-- -R -->
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229 <param name="max_reseed" type="integer" value="2"
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230 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/>
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231
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232 <param name="qupto" type="integer" value="0"
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233 label="Only aligns the first N reads or read pairs from the input"
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234 help="Default is 0 and means 'no-limit'."/>
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235 <param name="skip_reads" type="integer" value="0"
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236 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
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237
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238 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
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239 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
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240 help=""/>
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241 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
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242 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads"
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243 help=""/>
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244
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245 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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246 label="Write ambiguous reads to an extra output file"
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247 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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248 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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249 label="Write all reads that could not be aligned to a file"/>
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250 <!-- output Options -->
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251 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
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252 label="Write the bismark output and summary information to an extra file"/>
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253 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
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254 label="Offer all report files concatenated in one file (Mapping Report)"/>
27
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255 <param argument="--non-directional" name="non_directional" type="boolean"
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256 truevalue="--non-directional" falsevalue="" checked="false"
26
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257 label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
25
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258
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259 <!--end output options -->
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260 </when> <!-- full -->
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261 </conditional> <!-- params -->
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262 <!--
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263 <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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264 -->
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265 </inputs>
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266
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267
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268 <outputs>
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269 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
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270 <filter>
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271 ((
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272 params['settingsType'] == "default" or
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273 ( params['settingsType'] == "custom" and
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274 params['isReportOutput'] is True )
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275 ))
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276 </filter>
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277 </data>
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278 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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279 <filter>
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280 ((
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281 params['settingsType'] == "custom" and
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282 params['bismark_stdout'] is True
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283 ))
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284 </filter>
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285 </data>
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286
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287 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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288 <actions>
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289 <conditional name="refGenomeSource.genomeSource">
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290 <when value="built_in_indexes">
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291 <action type="metadata" name="dbkey">
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292 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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293 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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294 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
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295 </option>
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296 </action>
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297 </when>
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298 <when value="generate_indexes">
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299 <action type="metadata" name="dbkey">
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300 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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301 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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302 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
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303 </option>
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304 </action>
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305 </when>
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306 </conditional>
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307 </actions>
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308 <change_format>
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309 <when input="sort_bam" value="true" format="bam"/>
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310 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/>
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311 </change_format>
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312 </data>
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313
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314 <data format="fastq" name="output_suppressed_reads_l"
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315 label="${tool.name} on ${on_string}: suppressed reads (L)">
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316 <filter>
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317 ((
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318 params['settingsType'] == "custom" and
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319 params['suppressed_read_file'] is True
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320 ))
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321 </filter>
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322 <actions>
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323 <conditional name="singlePaired.sPaired">
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324 <when value="single">
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325 <action type="format">
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326 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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327 </action>
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328 </when>
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329 </conditional>
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330 </actions>
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331 </data>
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332
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333 <data format="fastq" name="output_suppressed_reads_r"
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334 label="${tool.name} on ${on_string}: suppressed reads (R)">
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335 <filter>
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336 ((
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337 singlePaired['sPaired'] == "paired" and
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338 params['settingsType'] == "custom" and
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339 params['suppressed_read_file'] is True
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340 ))
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341 </filter>
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342 <actions>
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343 <conditional name="singlePaired.sPaired">
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344 <when value="single">
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345 <action type="format">
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346 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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347 </action>
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348 </when>
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349 <!--when value="paired">
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350 <action type="format">
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351 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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352 </action>
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353 </when-->
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354 </conditional>
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355 </actions>
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356 </data>
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357
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358 <!-- Outout unmapped reads -->
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359 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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360 <filter>
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361 ((
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362 params['settingsType'] == "custom" and
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363 params['unmapped_read_file'] is True
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364 ))
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365 </filter>
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366 <actions>
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367 <conditional name="singlePaired.sPaired">
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368 <when value="single">
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369 <action type="format">
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370 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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371 </action>
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372 </when>
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373 <!--when value="paired">
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374 <action type="format">
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375 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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376 </action>
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377 </when-->
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378 </conditional>
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379 </actions>
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380 </data>
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381 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
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382 <filter>
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383 ((
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384 singlePaired['sPaired'] == "paired" and
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385 params['settingsType'] == "custom" and
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386 params['unmapped_read_file'] is True
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387 ))
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388 </filter>
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389 <actions>
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390 <conditional name="singlePaired.sPaired">
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391 <when value="single">
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392 <action type="format">
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393 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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394 </action>
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395 </when>
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396 <!--when value="paired">
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397 <action type="format">
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398 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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399 </action>
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400 </when-->
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401 </conditional>
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402 </actions>
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403 </data>
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404 </outputs>
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405 <tests>
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406 <test>
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407 <param name="genomeSource" value="history"/>
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408 <param name="own_file" value="mm10.tiny.fa.gz" />
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409 <param name="sPaired" value="single"/>
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410 <param name="input_singles" value="input1.fq.gz" ftype="fastqsanger"/>
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411 <param name="sort_bam" value="false"/>
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412 <param name="settingsType" value="custom"/>
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413 <param name="suppressed_read_file" value="true"/>
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414 <param name="unmapped_read_file" value="true"/>
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415 <param name="bismark_stdout" value="true"/>
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416 <param name="isReportOutput" value="true"/>
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417
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418 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80">
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419 <assert_contents>
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420 <has_text text="Sequences analysed in total:" />
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421 <has_text text="44115" />
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422 <has_text text="Mapping efficiency:" />
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423 <has_text text="1.3%" />
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424 <has_text text="Bismark run complete" />
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425 </assert_contents>
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426 </output>
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427 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
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428 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
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429 </test>
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430 </tests>
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431
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432 <help>
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433 <![CDATA[
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434
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435 **What it does**
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436
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437 | 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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438 | 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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439 | 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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440 | 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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441 |
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442 | 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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443 |
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444 | 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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445
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446 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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447
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448 ----
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449
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450 **Know what you are doing**
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451
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452 .. class:: warningmark
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453
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454 | 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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455 | In other words = running this tool with default parameters will probably not give you meaningful results.
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456 | 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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457 |
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458
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459 .. class:: warningmark
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460
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461 | 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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462
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463 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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464
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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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
bgruening
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467 **Input formats**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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468
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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469 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
470
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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471 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
472
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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473 **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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diff changeset
474
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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475 | 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
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476 | 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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477 | 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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diff changeset
478
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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479 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
480
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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481 **Outputs**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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482
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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483 * 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
484
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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485 Column Description
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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486 -------- --------------------------------------------------------
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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487 1 QNAME seq-ID
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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488 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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489 originated from into account
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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490 (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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491 3 RNAME chromosome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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492 4 POS start position
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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493 5 MAPQ always 255
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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494 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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495 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
bgruening
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496 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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497 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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498 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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499 11 QUAL Phred33 scale
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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500 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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501 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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502 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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503 14 XM-tag methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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504 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
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505 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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506
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
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508 | 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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509 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
510
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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511 * 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
512
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
513 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
514 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
bgruening
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515 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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diff changeset
516
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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diff changeset
518
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
519 **Note on Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
520
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
521 | 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
522
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
523 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
524
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
525 **Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
526
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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527 * **If Paired-End Reads**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
528
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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529 * **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
530
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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531 | 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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532 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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533 | 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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diff changeset
534
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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535
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
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536 * **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
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 | 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
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539 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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540 | 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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541
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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542
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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543 * **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
544
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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545 | 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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546 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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547 | 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
548
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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549 * **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
bgruening
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 | 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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552 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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553 | 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:
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554
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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555
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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556 * **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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557
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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558 | 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
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559 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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560 | 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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561
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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562 * **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
bgruening
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563
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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564 | <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
bgruening
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565 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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566 | 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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diff changeset
567
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
568 * **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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diff changeset
569
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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570 | 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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571 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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572 | Input option *-u/--upto <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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573
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
574 * **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
bgruening
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diff changeset
575
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
576 | Input option *-s/--skip*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
577
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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578 * **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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diff changeset
579
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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580 | 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
bgruening
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581 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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582 | 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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583
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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584 * **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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585
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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586 | 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
bgruening
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587 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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588 | Bowtie 2 Paired-End option *--no-mixed*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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589
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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590 * **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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591
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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592 | 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
bgruening
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593 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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594 | Output option *--ambiguous*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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595
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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596 * **Write all reads that could not be aligned to a file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
597
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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598 | 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
bgruening
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599 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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600 | Output option *-un/--unmapped*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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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 * **Offer all report files concatenated in one file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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603
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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604 | Prints out a Bismark mapping report
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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605
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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606 ]]>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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607 </help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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608 <citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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609 <citation type="doi">10.1093/bioinformatics/btr167</citation>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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610 </citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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611 </tool>