Mercurial > repos > bgruening > bismark

annotate bismark_mapping/bismark_bowtie2_wrapper.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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7
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.16.3">
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2
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3 <description>Bisulfite reads mapper</description>
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4 <!--<version_command>bismark version</version_command>-->
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5 <requirements>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 <requirement type="package" version="2.1.0">bowtie2</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <command interpreter="python">
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16 <![CDATA[
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17 bismark_wrapper.py
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18
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19 ## Change this to accommodate the number of threads you have available.
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20 --num-threads "\${GALAXY_SLOTS:-24}"
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21
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22 ##--bismark_path \$SCRIPT_PATH
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23 --bismark_path "$__tool_directory__"
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24
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25 --bowtie2
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26
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27 ##
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28 ## Bismark Genome Preparation, if desired.
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29 ##
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30
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31 ## Handle reference file.
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32 #if $refGenomeSource.genomeSource == "built_in_fasta":
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33 --own-file="${refGenomeSource.built_in_fasta.fields.path}"
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34 #else if $refGenomeSource.genomeSource == "own_fasta":
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35 --own-file="$refGenomeSource['own_fasta']"
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36 #else:
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37 --indexes-path "${refGenomeSource.built_in_indexes.fields.path}"
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38 #end if
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39
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40 ##
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41 ## Input parameters
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42 ##
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43
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44 #if $singlePaired.sPaired == "single":
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45 --single-paired $singlePaired.input_singles
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46
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47 #if $singlePaired.input_singles.ext == "fastqillumina":
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48 --phred64-quals
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49 --fastq
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50 #elif $singlePaired.input_singles.ext == "fastqsanger":
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51 --fastq
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52 #elif $singlePaired.input_singles.ext == "fasta":
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53 --fasta
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54 #end if
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55 #else:
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56 --mate-paired
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57 #set $mate1 = list()
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58 #set $mate2 = list()
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59 #for $mate_pair in $singlePaired.mate_list
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60 $mate1.append( str($mate_pair.input_mate1) )
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61 $mate2.append( str($mate_pair.input_mate2) )
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62 #end for
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63
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64 --mate1 #echo ','.join($mate1)
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65 --mate2 #echo ','.join($mate2)
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66
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67 #for $mate_pair in $singlePaired.mate_list:
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68 #if $mate_pair.input_mate1.ext == "fastqillumina":
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69 --phred64-quals
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70 --fastq
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71 #elif $mate_pair.input_mate1.ext == "fastqsanger":
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72 --fastq
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73 #elif $mate_pair.input_mate1.ext == "fasta":
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74 --fasta
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75 #end if
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76 #break
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77 #end for
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78
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79 -I $singlePaired.minInsert
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80 -X $singlePaired.maxInsert
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81 #end if
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82
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83 #if $sort_bam:
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84 --sort-bam
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85 #end if
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86
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87 ## for now hardcode the value for the required memory per thread in --best mode
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88 --chunkmbs 512
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89
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90
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91 #if $params.settingsType == "custom":
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92
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93 ## default 20
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94 --seed-len $params.seed_len
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95 ## default 0
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96 --seed-mismatches $params.seed_mismatches
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97 ## default 15
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98 --seed-extention-attempts $params.seed_extention_attempts
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99 ## default 2
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100 --max-reseed $params.max_reseed
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101
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102 ## default 70
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103 ##--maqerr $params.maqerr
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104
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105 ## default unlimited
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106 #if $params.qupto != 0:
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107 --qupto $params.qupto
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108 #end if
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109 #if $params.skip_reads != 0:
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110 --skip-reads $params.skip_reads
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111 #end if
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112
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113 ## if set, disable the original behaviour
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114 $params.no_mixed
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115 ## if set, disable the original behaviour
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116 $params.no_discordant
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117
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118 #if $params.bismark_stdout:
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119 --stdout "$output_stdout"
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120 #end if
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121
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122 #if $params.isReportOutput:
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123 --output-report-file "$report_file"
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124 #end if
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125
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126 #else:
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127 --output-report-file "$report_file"
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128 #end if
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129
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130 ##
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131 ## Output parameters.
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132 ##
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133 --output $output
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134 ##$suppress_header
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135
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136 #if str( $singlePaired.sPaired ) == "single"
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137 #if $output_unmapped_reads_l
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138 --output-unmapped-reads "$output_unmapped_reads_l"
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139 #end if
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140 #if $output_suppressed_reads_l
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141 --output-suppressed-reads "$output_suppressed_reads_l"
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142 #end if
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143 #else
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144 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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145 --output-unmapped-reads-l "$output_unmapped_reads_l"
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146 --output-unmapped-reads-r "$output_unmapped_reads_r"
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147 #end if
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148 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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149 --output-suppressed-reads-l "$output_suppressed_reads_l"
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150 --output-suppressed-reads-r "$output_suppressed_reads_r"
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151 #end if
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152 #end if
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153
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154 ]]>
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155 </command>
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156 <inputs>
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157 <conditional name="refGenomeSource">
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158 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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159 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
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160 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
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161 <option value="own_fasta">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
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162 </param>
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163 <when value="built_in_indexes">
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164 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)" help="If your genome of interest is not listed, contact your Galaxy admin">
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165 <options from_data_table="bismark_indexes">
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166 <filter type="sort_by" column="name"/>
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167 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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168 </options>
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169 </param>
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170 </when>
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171 <when value="built_in_fasta">
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172 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
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173 <options from_data_table="all_fasta">
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174 <filter type="sort_by" column="name"/>
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175 <validator type="no_options" message="No genomes in fasta are available for the selected input dataset"/>
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176 </options>
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177 </param>
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178 </when>
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179 <when value="own_fasta">
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180 <param name="own_fasta" type="data" format="fasta" label="Select the reference genome"/>
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181 </when>
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182 </conditional>
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183
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184 <!-- Input Parameters -->
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185 <conditional name="singlePaired">
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186 <param name="sPaired" type="select" label="Is this library mate-paired?">
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187 <option value="single">Single-end</option>
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188 <option value="paired">Paired-end</option>
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189 </param>
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190 <when value="single">
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191 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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192 </when>
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193 <when value="paired">
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194 <repeat name="mate_list" title="Paired End Pairs" min="1">
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195 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
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196 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
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197 </repeat>
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198 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
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199 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
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200 </when>
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201 </conditional>
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202
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203 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" 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" help="You can use the default settings or set custom values for any of Bismark's parameters.">
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207 <option value="default">Use Defaults</option>
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208 <option value="custom">Full parameter list</option>
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209 </param>
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210 <!--<when value="default" />-->
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211 <!-- Full/advanced params. -->
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212 <when value="custom">
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213 <!-- -N -->
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214 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
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215 <!-- -L -->
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216 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
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217 <!--
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218 <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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219 -->
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220 <!-- -D -->
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221 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
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222 <!-- -R -->
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223 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
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224
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225 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
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226 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
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227
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228 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)" help="" />
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229 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads" help="" />
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230
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231 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
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232 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" />
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233 <!-- output Options -->
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234 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
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235 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Offer all report files concatenated in one file (Mapping Report)" />
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236
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237 <!--end output options -->
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238 </when> <!-- full -->
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239 </conditional> <!-- params -->
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240 <!--
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241 <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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242 -->
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243 </inputs>
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244
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245
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246 <outputs>
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247 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
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248 <filter>
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249 ((
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250 params['settingsType'] == "default" or
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251 ( params['settingsType'] == "custom" and
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252 params['isReportOutput'] is True )
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253 ))
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254 </filter>
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255 </data>
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256 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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257 <filter>
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258 ((
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259 params['settingsType'] == "custom" and
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260 params['bismark_stdout'] is True
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261 ))
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262 </filter>
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263 </data>
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264
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265 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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266 <actions>
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267 <conditional name="refGenomeSource.genomeSource">
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268 <when value="built_in_indexes">
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269 <action type="metadata" name="dbkey">
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270 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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271 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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272 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
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273 </option>
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274 </action>
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275 </when>
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276 <when value="generate_indexes">
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277 <action type="metadata" name="dbkey">
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278 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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279 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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280 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
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281 </option>
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282 </action>
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283 </when>
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284 </conditional>
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285 </actions>
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286 </data>
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287
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288 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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289 <filter>
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290 ((
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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291 params['settingsType'] == "custom" and
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292 params['suppressed_read_file'] is True
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293 ))
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294 </filter>
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295 <actions>
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296 <conditional name="singlePaired.sPaired">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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297 <when value="single">
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298 <action type="format">
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299 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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300 </action>
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301 </when>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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302 </conditional>
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303 </actions>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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304 </data>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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305
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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306 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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307 <filter>
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308 ((
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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309 singlePaired['sPaired'] == "paired" and
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310 params['settingsType'] == "custom" and
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311 params['suppressed_read_file'] is True
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312 ))
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313 </filter>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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314 <actions>
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315 <conditional name="singlePaired.sPaired">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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316 <when value="single">
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317 <action type="format">
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318 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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319 </action>
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320 </when>
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321 <when value="paired">
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322 <!--action type="format">
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323 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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324 </action-->
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325 </when>
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326 </conditional>
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327 </actions>
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328 </data>
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329
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330 <!-- Outout unmapped reads -->
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331 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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332 <filter>
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333 ((
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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334 params['settingsType'] == "custom" and
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335 params['unmapped_read_file'] is True
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336 ))
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337 </filter>
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338 <actions>
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339 <conditional name="singlePaired.sPaired">
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340 <when value="single">
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341 <action type="format">
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342 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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343 </action>
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344 </when>
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345 <when value="paired">
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346 <!--action type="format">
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bgruening
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347 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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348 </action-->
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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349 </when>
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350 </conditional>
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351 </actions>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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352 </data>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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353
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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354 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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355 <filter>
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356 ((
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357 singlePaired['sPaired'] == "paired" and
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358 params['settingsType'] == "custom" and
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359 params['unmapped_read_file'] is True
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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360 ))
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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361 </filter>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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362 <actions>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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363 <conditional name="singlePaired.sPaired">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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364 <when value="single">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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365 <action type="format">
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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366 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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367 </action>
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368 </when>
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369 <when value="paired">
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370 <!--action type="format">
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371 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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372 </action-->
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373 </when>
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374 </conditional>
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375 </actions>
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376 </data>
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377 </outputs>
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378
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379 <tests>
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380 </tests>
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381
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382 <help>
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383 <![CDATA[
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384
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385 **What it does**
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386
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387 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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388 | 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).
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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389 | 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).
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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390 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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391 |
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392 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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393 |
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394 | 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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395
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396 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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397
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398 ----
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399
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400 **Know what you are doing**
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401
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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402 .. class:: warningmark
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403
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404 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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405 | In other words = running this tool with default parameters will probably not give you meaningful results.
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406 | A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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407 |
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diff changeset
408
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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409 .. class:: warningmark
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diff changeset
410
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411 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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412
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413 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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414
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415 ----
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diff changeset
416
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417 **Input formats**
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418
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419 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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diff changeset
420
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421 ----
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422
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423 **A Note on Built-in Reference Genomes**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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424
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425 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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426 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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427 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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parents:
diff changeset
428
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429 ----
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diff changeset
430
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431 **Outputs**
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432
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433 * The final output of Bismark is in SAM format by default, and has the following columns::
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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diff changeset
434
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bgruening
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435 Column Description
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436 -------- --------------------------------------------------------
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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437 1 QNAME seq-ID
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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438 2 FLAG this flag tries to take the strand a bisulfite read
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
439 originated from into account
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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440 (this is different from ordinary DNA alignment flags!)
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441 3 RNAME chromosome
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442 4 POS start position
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443 5 MAPQ always 255
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diff changeset
444 6 CIGAR extended CIGAR string
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
445 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
446 8 MPOS 1-based Mate POSition
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
447 9 ISIZE Inferred insert SIZE
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
448 10 SEQ query SEQuence on the same strand as the reference
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
449 11 QUAL Phred33 scale
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
450 12 NM-tag edit distance to the reference)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
451 13 XX-tag base-by-base mismatches to the reference.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
452 This does not include indels.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
453 14 XM-tag methylation call string
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
454 15 XR-tag read conversion state for the alignment
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
455 16 XG-tag genome conversion state for the alignment
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
456
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
457
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
458 | Each read of paired-end alignments is written out in a separate line in the above format.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
459 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
460
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
461 * It looks like this (scroll sideways to see the entire example)::
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
462
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
463 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
464 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
465 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
466
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
467 ----
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
468
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
469 **Note on Bismark settings**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
470
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
471 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
472
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
473 ----
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
474
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
475 **Bismark settings**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
476
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
477 * **If Paired-End Reads**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
478
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
479 * **Minimum insert size for valid paired-end alignments**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
480
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
481 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
482 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
483 | Alignment option *-I/--minins <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
484
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
485
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
486 * **Maximum insert size for valid paired-end alignments**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
487
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
488 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
489 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
490 | Alignment option *-X/--maxins <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
491
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
492
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
493 * **Number of mismatches to be allowed in a seed alignment during multiseed alignment**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
494
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
495 | 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).
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
496 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
497 | Bowtie 2 Specific option *-N <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
498
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
499 * **Length of the seed substrings to align during multiseed alignment**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
500
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
501 | 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).
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
502 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
503 | Bowtie 2 Specific option *-L <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
504
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
505
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
506 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
507
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
508 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
509 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
510 | Bowtie 2 Effort option *-D <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
511
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
512 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
513
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
514 | <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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
515 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
516 | Bowtie 2 Effort option *-R <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
517
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
518 * **Only aligns the first N reads or read pairs from the input**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
519
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
520 | Only aligns the first <int> reads or read pairs from the input. Default: no limit.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
521 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
522 | Input option *-u/--upto <INT>*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
523
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
524 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
525
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
526 | Input option *-s/--skip*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
527
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
528 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
529
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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530 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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531 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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532 | Bowtie 2 Paired-End option *--no-discordant*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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533
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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534 * **Disable Bowtie 2's behaviour to try to find alignments for the individual mates**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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535
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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536 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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537 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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538 | Bowtie 2 Paired-End option *--no-mixed*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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539
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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540 * **Write ambiguous reads to an extra output file**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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541
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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542 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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543 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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544 | Output option *--ambiguous*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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545
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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546 * **Write all reads that could not be aligned to a file**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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547
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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548 | 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.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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549 |
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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550 | Output option *-un/--unmapped*
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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551
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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552 * **Offer all report files concatenated in one file**
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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553
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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554 | Prints out a Bismark mapping report
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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555
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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556 ]]>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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557 </help>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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558 <citations>
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559 <citation type="doi">10.1093/bioinformatics/btr167</citation>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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560 </citations>
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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561 </tool>