Mercurial > repos > bgruening > bismark

annotate bismark_bowtie2_wrapper.xml @ 31:45b1a9520fa9 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
author bgruening
date Tue, 30 Jul 2019 10:32:37 -0400
parents 50c594522ed2
children c5003e3c507d
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45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" 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="0.22.1">bismark</requirement>
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5 <requirement type="package" version="1.8">samtools</requirement>
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6 <requirement type="package" version="2.3.5">bowtie2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 #import re
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10
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11 #if $singlePaired.sPaired == "single":
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12 #if $singlePaired.input_singles.ext == "fasta":
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13 #set read1 = 'input_1.fa'
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14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
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15 #set read1 = 'input_1.fq.gz'
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16 #else
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17 #set read1 = 'input_1.fq'
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18 #end if
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19 ln -s '${singlePaired.input_singles}' ${read1} &&
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20 #else:
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21 #set $mate1 = list()
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22 #set $mate2 = list()
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23 #for $mate_pair in $singlePaired.mate_list
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25 #if $mate_pair.input_mate1.ext == "fasta":
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26 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
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27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
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28 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
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29 #else
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30 #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
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31 #end if
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32 ln -s '${mate_pair.input_mate1}' ${read1} &&
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34 #if $mate_pair.input_mate2.ext == "fasta":
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35 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
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36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
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37 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
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38 #else
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39 #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
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40 #end if
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41 ln -s '${mate_pair.input_mate2}' ${read2} &&
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43 $mate1.append( str($read1) )
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44 $mate2.append( str($read2) )
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45 #end for
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46 #end if
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47
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48 python '$__tool_directory__/bismark_wrapper.py'
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50 ## Change this to accommodate the number of threads you have available.
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51 --num-threads "\${GALAXY_SLOTS:-4}"
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53 ##
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54 ## Bismark Genome Preparation, if desired.
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55 ##
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57 ## Handle reference file.
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58 #if $refGenomeSource.genomeSource == "built_in_fasta":
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59 --own-file '${refGenomeSource.built_in_fasta.fields.path}'
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60 #else if $refGenomeSource.genomeSource == "history":
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61 --own-file '$refGenomeSource["own_file"]'
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62 #else:
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63 --indexes-path '${refGenomeSource.built_in_indexes.fields.path}'
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64 #end if
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66 ##
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67 ## Input parameters
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68 ##
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70 #if $singlePaired.sPaired == "single":
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71 --single-paired '${read1}'
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73 #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]:
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74 --phred64-quals
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75 --fastq
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76 #elif $singlePaired.input_singles.ext in ["fastqsanger", "fastqsanger.gz"]:
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77 --fastq
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78 #elif $singlePaired.input_singles.ext == "fasta":
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79 --fasta
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80 #end if
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81 #else:
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82 --mate-paired
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84 --mate1 #echo ','.join($mate1)
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85 --mate2 #echo ','.join($mate2)
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87 #for $mate_pair in $singlePaired.mate_list:
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88 #if $mate_pair.input_mate1.ext == "fastqillumina":
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89 --phred64-quals
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90 --fastq
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91 #elif $mate_pair.input_mate1.ext in "fastqsanger,fastqsanger.gz":
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92 --fastq
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93 #elif $mate_pair.input_mate1.ext == "fasta":
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94 --fasta
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95 #end if
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96 #break
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97 #end for
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98
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99 -I $singlePaired.minInsert
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100 -X $singlePaired.maxInsert
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101 #end if
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102
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103 #if $sort_bam:
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104 --sort-bam
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105 #end if
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106
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107 ## for now hardcode the value for the required memory per thread in --best mode
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108 --chunkmbs 512
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109
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110
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111 #if $params.settingsType == "custom":
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112
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113 ## default 20
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114 --seed-len $params.seed_len
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115 ## default 0
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116 --seed-mismatches $params.seed_mismatches
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117 ## default 15
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118 --seed-extention-attempts $params.seed_extention_attempts
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119 ## default 2
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120 --max-reseed $params.max_reseed
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121
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122 ## default 70
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123 ##--maqerr $params.maqerr
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124
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125 ## default unlimited
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126 #if $params.qupto != 0:
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127 --qupto $params.qupto
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128 #end if
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129 #if $params.skip_reads != 0:
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130 --skip-reads $params.skip_reads
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131 #end if
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132
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133 ## if set, disable the original behaviour
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134 $params.no_mixed
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135 ## if set, disable the original behaviour
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136 $params.no_discordant
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137
26
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138 $params.non_directional
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139
25
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140 #if $params.bismark_stdout:
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141 --stdout '$output_stdout'
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142 #end if
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143
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144 #if $params.isReportOutput:
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145 --output-report-file '$report_file'
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146 #end if
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147
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148 #else:
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149 --output-report-file '$report_file'
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150 #end if
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151
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152 ##
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153 ## Output parameters.
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154 ##
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155 --output '$output'
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156 ##$suppress_header
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157
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158 #if str( $singlePaired.sPaired ) == "single"
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159 #if $output_unmapped_reads_l
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160 --output-unmapped-reads '$output_unmapped_reads_l'
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161 #end if
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162 #if $output_suppressed_reads_l
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163 --output-suppressed-reads '$output_suppressed_reads_l'
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164 #end if
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165 #else
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166 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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167 --output-unmapped-reads-l '$output_unmapped_reads_l'
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168 --output-unmapped-reads-r '$output_unmapped_reads_r'
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169 #end if
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170 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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171 --output-suppressed-reads-l '$output_suppressed_reads_l'
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172 --output-suppressed-reads-r '$output_suppressed_reads_r'
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173 #end if
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174 #end if
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175
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176 ]]>
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177 </command>
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178 <inputs>
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179 <conditional name="refGenomeSource">
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180 <param name="genomeSource" type="select"
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181 label="Will you select a reference genome from your history or use a built-in index?"
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182 help="Built-ins were indexed using default options">
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183 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
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184 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
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185 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
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186 </param>
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187 <when value="built_in_indexes">
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188 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)"
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189 help="If your genome of interest is not listed, contact your Galaxy admin">
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190 <options from_data_table="bismark_indexes">
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191 <filter type="sort_by" column="name"/>
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192 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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193 </options>
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194 </param>
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195 </when>
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196 <when value="built_in_fasta">
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197 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
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198 <options from_data_table="all_fasta">
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199 <filter type="sort_by" column="name"/>
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200 <validator type="no_options"
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201 message="No genomes in fasta are available for the selected input dataset"/>
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202 </options>
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203 </param>
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204 </when>
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205 <when value="history">
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206 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
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207 </when>
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208 </conditional>
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209
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210 <!-- Input Parameters -->
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211 <conditional name="singlePaired">
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212 <param name="sPaired" type="select" label="Is this library mate-paired?">
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213 <option value="single">Single-end</option>
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214 <option value="paired">Paired-end</option>
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215 </param>
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216 <when value="single">
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217 <param name="input_singles" type="data"
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218 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file"
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219 help="FASTQ or FASTA files."/>
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220 </when>
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221 <when value="paired">
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222 <repeat name="mate_list" title="Paired End Pairs" min="1">
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223 <param name="input_mate1" type="data"
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224 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1"
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225 help="FASTQ or FASTA files."/>
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226 <param name="input_mate2" type="data"
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227 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2"
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228 help="FASTQ or FASTA files."/>
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229 </repeat>
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230 <param name="minInsert" type="integer" value="0"
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231 label="Minimum insert size for valid paired-end alignments"/>
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232 <param name="maxInsert" type="integer" value="500"
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233 label="Maximum insert size for valid paired-end alignments"/>
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234 </when>
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235 </conditional>
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236
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237 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False"
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238 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
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239
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240 <conditional name="params">
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241 <param name="settingsType" type="select" label="Bismark settings to use"
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242 help="You can use the default settings or set custom values for any of Bismark's parameters.">
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243 <option value="default">Use Defaults</option>
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244 <option value="custom">Full parameter list</option>
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245 </param>
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246 <!-- Full/advanced params. -->
28
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247 <when value="default"></when>
25
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248 <when value="custom">
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249 <!-- -N -->
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250 <param name="seed_mismatches" type="integer" value="0"
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251 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
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252 <!-- -L -->
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253 <param name="seed_len" type="integer" value="20"
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254 label="Length of the seed substrings to align during multiseed alignment"/>
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255 <!--
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256 <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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257 -->
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258 <!-- -D -->
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259 <param name="seed_extention_attempts" type="integer" value="15"
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260 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
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261 <!-- -R -->
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262 <param name="max_reseed" type="integer" value="2"
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263 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/>
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264
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265 <param name="qupto" type="integer" value="0"
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266 label="Only aligns the first N reads or read pairs from the input"
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267 help="Default is 0 and means 'no-limit'."/>
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268 <param name="skip_reads" type="integer" value="0"
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269 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
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270
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271 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
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272 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
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273 help=""/>
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274 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
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275 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads"
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276 help=""/>
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277
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278 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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279 label="Write ambiguous reads to an extra output file"
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280 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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281 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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282 label="Write all reads that could not be aligned to a file"/>
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283 <!-- output Options -->
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284 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
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285 label="Write the bismark output and summary information to an extra file"/>
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286 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
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287 label="Offer all report files concatenated in one file (Mapping Report)"/>
27
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288 <param argument="--non-directional" name="non_directional" type="boolean"
28
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289 truevalue="--non-directional" falsevalue="" checked="false"
26
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290 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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291
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292 <!--end output options -->
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293 </when> <!-- full -->
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294 </conditional> <!-- params -->
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295 <!--
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296 <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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297 -->
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298 </inputs>
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299
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300
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301 <outputs>
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302 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
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303 <filter>
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304 ((
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305 params['settingsType'] == "default" or
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306 ( params['settingsType'] == "custom" and
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307 params['isReportOutput'] is True )
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308 ))
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309 </filter>
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310 </data>
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311 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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312 <filter>
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313 ((
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314 params['settingsType'] == "custom" and
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315 params['bismark_stdout'] is True
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316 ))
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317 </filter>
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318 </data>
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319
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320 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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321 <actions>
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322 <conditional name="refGenomeSource.genomeSource">
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323 <when value="built_in_indexes">
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324 <action type="metadata" name="dbkey">
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325 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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326 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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327 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
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328 </option>
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329 </action>
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330 </when>
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331 <when value="generate_indexes">
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332 <action type="metadata" name="dbkey">
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333 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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334 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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335 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
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336 </option>
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337 </action>
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338 </when>
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339 </conditional>
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340 </actions>
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341 <change_format>
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342 <when input="sort_bam" value="true" format="bam"/>
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343 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/>
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344 </change_format>
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345 </data>
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346
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347 <data format="fastq" name="output_suppressed_reads_l"
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348 label="${tool.name} on ${on_string}: suppressed reads (L)">
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349 <filter>
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350 ((
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351 params['settingsType'] == "custom" and
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352 params['suppressed_read_file'] is True
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353 ))
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354 </filter>
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355 <actions>
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356 <conditional name="singlePaired.sPaired">
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357 <when value="single">
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358 <action type="format">
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359 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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360 </action>
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361 </when>
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362 </conditional>
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363 </actions>
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364 </data>
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365
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366 <data format="fastq" name="output_suppressed_reads_r"
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367 label="${tool.name} on ${on_string}: suppressed reads (R)">
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368 <filter>
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369 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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370 singlePaired['sPaired'] == "paired" and
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371 params['settingsType'] == "custom" and
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372 params['suppressed_read_file'] is True
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373 ))
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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374 </filter>
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375 <actions>
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376 <conditional name="singlePaired.sPaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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377 <when value="single">
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diff changeset
378 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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379 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
380 </action>
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381 </when>
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382 <!--when value="paired">
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parents:
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383 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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384 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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385 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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386 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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387 </conditional>
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388 </actions>
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389 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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390
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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391 <!-- Outout unmapped reads -->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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392 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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393 <filter>
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394 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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395 params['settingsType'] == "custom" and
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396 params['unmapped_read_file'] is True
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397 ))
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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398 </filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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399 <actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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400 <conditional name="singlePaired.sPaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
401 <when value="single">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
402 <action type="format">
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403 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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404 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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405 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
406 <!--when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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407 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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408 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
409 </action>
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410 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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411 </conditional>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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412 </actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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413 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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414 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
415 <filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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416 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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417 singlePaired['sPaired'] == "paired" and
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418 params['settingsType'] == "custom" and
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419 params['unmapped_read_file'] is True
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420 ))
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421 </filter>
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diff changeset
422 <actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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423 <conditional name="singlePaired.sPaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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424 <when value="single">
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parents:
diff changeset
425 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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426 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
427 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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428 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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429 <!--when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
430 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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431 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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432 </action>
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433 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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434 </conditional>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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435 </actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
436 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
437 </outputs>
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438 <tests>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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439 <test>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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440 <param name="genomeSource" value="history"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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441 <param name="own_file" value="mm10.tiny.fa.gz" />
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442 <param name="sPaired" value="single"/>
30
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
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diff changeset
443 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
25
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444 <param name="sort_bam" value="false"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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445 <param name="settingsType" value="custom"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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446 <param name="suppressed_read_file" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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447 <param name="unmapped_read_file" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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448 <param name="bismark_stdout" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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449 <param name="isReportOutput" value="true"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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450
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451 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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452 <assert_contents>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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453 <has_text text="Sequences analysed in total:" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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454 <has_text text="44115" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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455 <has_text text="Mapping efficiency:" />
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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456 <has_text text="1.3%" />
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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457 <has_text text="Bismark run complete" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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458 </assert_contents>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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459 </output>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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460 <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
461 <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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462 </test>
30
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463 <test>
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464 <param name="genomeSource" value="history"/>
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465 <param name="own_file" value="mm10.tiny.fa.gz" />
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466 <param name="sPaired" value="single"/>
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467 <param name="input_singles" value="input1.fq" ftype="fastqsanger"/>
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468 <param name="sort_bam" value="false"/>
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469 <param name="settingsType" value="custom"/>
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470 <param name="suppressed_read_file" value="true"/>
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471 <param name="unmapped_read_file" value="true"/>
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472 <param name="bismark_stdout" value="true"/>
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473 <param name="isReportOutput" value="true"/>
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474
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475 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80">
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476 <assert_contents>
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477 <has_text text="Sequences analysed in total:" />
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478 <has_text text="1000" />
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479 <has_text text="Mapping efficiency:" />
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480 <has_text text="0.8%" />
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481 <has_text text="Bismark run complete" />
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482 </assert_contents>
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483 </output>
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484 <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/>
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485 <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
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486 </test>
31
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487 <test>
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488 <param name="genomeSource" value="history"/>
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489 <param name="own_file" value="mm10.tiny.fa.gz" />
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490 <param name="sPaired" value="paired"/>
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491 <repeat name="mate_list">
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492 <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/>
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493 <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/>
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494 </repeat>
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495 <param name="sort_bam" value="false"/>
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496 <param name="settingsType" value="custom"/>
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497 <param name="suppressed_read_file" value="true"/>
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498 <param name="unmapped_read_file" value="true"/>
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499 <param name="bismark_stdout" value="true"/>
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500 <param name="isReportOutput" value="true"/>
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501
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502 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80">
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503 <assert_contents>
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504 <has_text text="Sequence pairs analysed in total:" />
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505 <has_text text="1000" />
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506 <has_text text="Mapping efficiency:" />
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507 <has_text text="0.0%" />
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508 <has_text text="Bismark run complete" />
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509 </assert_contents>
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510 </output>
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511 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
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512 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
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513 </test>
25
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514 </tests>
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515
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516 <help>
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517 <![CDATA[
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518
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519 **What it does**
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520
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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521 | 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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522 | 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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523 | 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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524 | 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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525 |
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526 | 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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527 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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528 | 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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529
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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530 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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531
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532 ----
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533
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534 **Know what you are doing**
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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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536 .. class:: warningmark
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537
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538 | 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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539 | In other words = running this tool with default parameters will probably not give you meaningful results.
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540 | 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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541 |
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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 .. class:: warningmark
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544
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545 | 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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546
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547 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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548
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549 ----
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550
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551 **Input formats**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
552
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
553 | 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
554
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
555 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
556
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
557 **A Note on Built-in Reference Genomes**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
558
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
559 | The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
560 | 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
parents:
diff changeset
561 | 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
bgruening
parents:
diff changeset
562
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
563 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
564
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
565 **Outputs**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
566
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
567 * 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
bgruening
parents:
diff changeset
568
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
569 Column Description
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
570 -------- --------------------------------------------------------
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
571 1 QNAME seq-ID
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
572 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
bgruening
parents:
diff changeset
573 originated from into account
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
574 (this is different from ordinary DNA alignment flags!)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
575 3 RNAME chromosome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
576 4 POS start position
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
577 5 MAPQ always 255
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
578 6 CIGAR extended CIGAR string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
579 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
parents:
diff changeset
580 8 MPOS 1-based Mate POSition
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
581 9 ISIZE Inferred insert SIZE
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
582 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
bgruening
parents:
diff changeset
583 11 QUAL Phred33 scale
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
584 12 NM-tag edit distance to the reference)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
585 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
bgruening
parents:
diff changeset
586 This does not include indels.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
587 14 XM-tag methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
588 15 XR-tag read conversion state for the alignment
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
589 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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parents:
diff changeset
590
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
591
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
592 | 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
bgruening
parents:
diff changeset
593 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
594
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
595 * 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
bgruening
parents:
diff changeset
596
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
597 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
parents:
diff changeset
598 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
parents:
diff changeset
599 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
600
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
601 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
602
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
603 **Note on Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
604
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
605 | 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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parents:
diff changeset
606
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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diff changeset
607 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
608
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
609 **Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
610
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
611 * **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
612
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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613 * **Minimum insert size for valid paired-end alignments**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
614
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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615 | 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
bgruening
parents:
diff changeset
616 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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617 | Alignment option *-I/--minins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
618
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
619
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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620 * **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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parents:
diff changeset
621
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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622 | The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. Default: 500.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
623 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
624 | Alignment option *-X/--maxins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
625
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
626
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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627 * **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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parents:
diff changeset
628
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
629 | Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for Bowtie 1 see -n).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
630 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
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631 | 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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diff changeset
632
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
633 * **Length of the seed substrings to align during multiseed alignment**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
634
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
635 | 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
bgruening
parents:
diff changeset
636 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
637 | Bowtie 2 Specific option *-L <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
638
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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639
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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parents:
diff changeset
640 * **How many consecutive seed extension attempts can fail before Bowtie 2 moves on**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
641
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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642 | 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.
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643 |
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644 | Bowtie 2 Effort option *-D <INT>*
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645
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646 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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647
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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648 | <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default: 2.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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649 |
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650 | Bowtie 2 Effort option *-R <INT>*
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651
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652 * **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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653
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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654 | 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
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655 |
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656 | Input option *-u/--upto <INT>*
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657
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658 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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659
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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660 | Input option *-s/--skip*
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661
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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662 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
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663
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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664 | Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior and it is on by default.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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665 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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666 | 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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667
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668 * **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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669
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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670 | 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.
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671 |
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672 | Bowtie 2 Paired-End option *--no-mixed*
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673
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674 * **Write ambiguous reads to an extra output file**
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675
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676 | 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.
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677 |
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678 | Output option *--ambiguous*
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679
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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680 * **Write all reads that could not be aligned to a file**
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681
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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682 | 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.
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683 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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684 | Output option *-un/--unmapped*
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685
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686 * **Offer all report files concatenated in one file**
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687
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688 | Prints out a Bismark mapping report
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689
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690 ]]>
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691 </help>
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692 <citations>
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693 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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694 </citations>
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695 </tool>