Mercurial > repos > bgruening > bismark

annotate bismark_bowtie2_wrapper.xml @ 33:f06523fe7828 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
author bgruening
date Wed, 21 Aug 2019 12:59:22 -0400
parents c5003e3c507d
children e5105f7e7b0d
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f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
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1 <tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy3" 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 $mate_pair.input_mate1.ext == "fasta":
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26 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
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27 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
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28 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
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29 #else
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30 #set read1 = re.sub('[^\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 $mate_pair.input_mate2.ext == "fasta":
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35 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
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36 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
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37 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
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38 #else
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39 #set read2 = re.sub('[^\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 unlimited
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123 #if $params.qupto != 0:
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124 --qupto $params.qupto
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125 #end if
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126 #if $params.skip_reads != 0:
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127 --skip-reads $params.skip_reads
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128 #end if
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129
33
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130 #if $params.score_min != "":
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131 --score-min '${params.score_min}'
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132 #end if
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133
25
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134 ## if set, disable the original behaviour
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135 $params.no_mixed
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136 ## if set, disable the original behaviour
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137 $params.no_discordant
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138
26
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139 $params.non_directional
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140
25
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141 #if $params.bismark_stdout:
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142 --stdout '$output_stdout'
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143 #end if
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144
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145 #if $params.isReportOutput:
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146 --output-report-file '$report_file'
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147 #end if
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148
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149 #else:
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150 --output-report-file '$report_file'
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151 #end if
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152
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153 ##
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154 ## Output parameters.
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155 ##
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156 --output '$output'
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157 ##$suppress_header
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158
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159 #if str( $singlePaired.sPaired ) == "single"
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160 #if $output_unmapped_reads_l
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161 --output-unmapped-reads '$output_unmapped_reads_l'
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162 #end if
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163 #if $output_suppressed_reads_l
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164 --output-suppressed-reads '$output_suppressed_reads_l'
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165 #end if
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166 #else
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167 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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168 --output-unmapped-reads-l '$output_unmapped_reads_l'
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169 --output-unmapped-reads-r '$output_unmapped_reads_r'
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170 #end if
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171 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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172 --output-suppressed-reads-l '$output_suppressed_reads_l'
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173 --output-suppressed-reads-r '$output_suppressed_reads_r'
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174 #end if
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175 #end if
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176
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177 ]]>
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178 </command>
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179 <inputs>
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180 <conditional name="refGenomeSource">
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181 <param name="genomeSource" type="select"
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182 label="Will you select a reference genome from your history or use a built-in index?"
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183 help="Built-ins were indexed using default options">
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184 <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
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185 <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
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186 <option value="history">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
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187 </param>
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188 <when value="built_in_indexes">
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189 <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)"
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190 help="If your genome of interest is not listed, contact your Galaxy admin">
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191 <options from_data_table="bismark_indexes">
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192 <filter type="sort_by" column="name"/>
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193 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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194 </options>
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195 </param>
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196 </when>
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197 <when value="built_in_fasta">
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198 <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
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199 <options from_data_table="all_fasta">
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200 <filter type="sort_by" column="name"/>
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201 <validator type="no_options"
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202 message="No genomes in fasta are available for the selected input dataset"/>
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203 </options>
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204 </param>
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205 </when>
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206 <when value="history">
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207 <param name="own_file" type="data" format="fasta" label="Select the reference genome"/>
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208 </when>
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209 </conditional>
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210
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211 <!-- Input Parameters -->
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212 <conditional name="singlePaired">
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213 <param name="sPaired" type="select" label="Is this library mate-paired?">
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214 <option value="single">Single-end</option>
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215 <option value="paired">Paired-end</option>
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216 </param>
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217 <when value="single">
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218 <param name="input_singles" type="data"
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219 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="FASTQ/FASTA file"
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220 help="FASTQ or FASTA files."/>
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221 </when>
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222 <when value="paired">
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223 <repeat name="mate_list" title="Paired End Pairs" min="1">
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224 <param name="input_mate1" type="data"
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225 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 1"
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226 help="FASTQ or FASTA files."/>
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227 <param name="input_mate2" type="data"
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228 format="fastqsanger,fastqillumina,fastq,fasta,fastq.gz,fastqsanger.gz" label="Mate pair 2"
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229 help="FASTQ or FASTA files."/>
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230 </repeat>
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231 <param name="minInsert" type="integer" value="0"
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232 label="Minimum insert size for valid paired-end alignments"/>
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233 <param name="maxInsert" type="integer" value="500"
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234 label="Maximum insert size for valid paired-end alignments"/>
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235 </when>
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236 </conditional>
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237
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238 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False"
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239 label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
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240
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241 <conditional name="params">
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242 <param name="settingsType" type="select" label="Bismark settings to use"
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243 help="You can use the default settings or set custom values for any of Bismark's parameters.">
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244 <option value="default">Use Defaults</option>
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245 <option value="custom">Full parameter list</option>
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246 </param>
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247 <!-- Full/advanced params. -->
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248 <when value="default"></when>
25
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249 <when value="custom">
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250 <!-- -N -->
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251 <param name="seed_mismatches" type="integer" value="0"
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252 label="Number of mismatches to be allowed in a seed alignment during multiseed alignment"/>
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253 <!-- -L -->
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254 <param name="seed_len" type="integer" value="20"
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255 label="Length of the seed substrings to align during multiseed alignment"/>
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256
25
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257 <!-- -D -->
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258 <param name="seed_extention_attempts" type="integer" value="15"
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259 label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on"/>
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260 <!-- -R -->
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261 <param name="max_reseed" type="integer" value="2"
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262 label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds"/>
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263
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264 <param name="qupto" type="integer" value="0"
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265 label="Only aligns the first N reads or read pairs from the input"
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266 help="Default is 0 and means 'no-limit'."/>
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267 <param name="skip_reads" type="integer" value="0"
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268 label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>
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269
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270 <param argument="--score-min" name="score_min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/>
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271
25
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272 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
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273 label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
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274 help=""/>
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275 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false"
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276 label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates (only for paired-end reads"
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277 help=""/>
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278
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279 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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280 label="Write ambiguous reads to an extra output file"
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281 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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282 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
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283 label="Write all reads that could not be aligned to a file"/>
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284 <!-- output Options -->
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285 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false"
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286 label="Write the bismark output and summary information to an extra file"/>
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287 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
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288 label="Offer all report files concatenated in one file (Mapping Report)"/>
27
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289 <param argument="--non-directional" name="non_directional" type="boolean"
28
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290 truevalue="--non-directional" falsevalue="" checked="false"
26
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291 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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292
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293 <!--end output options -->
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294 </when> <!-- full -->
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295 </conditional> <!-- params -->
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296 <!--
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297 <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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298 -->
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299 </inputs>
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300
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301
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302 <outputs>
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303 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
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304 <filter>
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305 ((
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306 params['settingsType'] == "default" or
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307 ( params['settingsType'] == "custom" and
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308 params['isReportOutput'] is True )
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309 ))
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310 </filter>
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311 </data>
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312 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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313 <filter>
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314 ((
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315 params['settingsType'] == "custom" and
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316 params['bismark_stdout'] is True
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317 ))
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318 </filter>
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319 </data>
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320
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321 <data format="qname_input_sorted.bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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322 <actions>
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323 <conditional name="refGenomeSource.genomeSource">
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324 <when value="built_in_indexes">
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325 <action type="metadata" name="dbkey">
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326 <option type="from_data_table" name="bismark_indexes" column="1" offset="0">
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327 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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328 <filter type="param_value" ref="refGenomeSource.built_in_indexes" column="0"/>
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329 </option>
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330 </action>
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331 </when>
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332 <when value="generate_indexes">
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333 <action type="metadata" name="dbkey">
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334 <option type="from_data_table" name="all_fasta" column="1" offset="0">
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335 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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336 <filter type="param_value" ref="refGenomeSource.generate_indexes" column="0"/>
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337 </option>
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338 </action>
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339 </when>
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340 </conditional>
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341 </actions>
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342 <change_format>
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343 <when input="sort_bam" value="true" format="bam"/>
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344 <when input="sort_bam" value="false" format="qname_input_sorted.bam"/>
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345 </change_format>
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346 </data>
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347
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348 <data format="fastq" name="output_suppressed_reads_l"
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349 label="${tool.name} on ${on_string}: suppressed reads (L)">
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350 <filter>
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351 ((
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352 params['settingsType'] == "custom" and
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353 params['suppressed_read_file'] is True
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354 ))
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355 </filter>
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356 <actions>
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357 <conditional name="singlePaired.sPaired">
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358 <when value="single">
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359 <action type="format">
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360 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext"/>
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361 </action>
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362 </when>
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363 </conditional>
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364 </actions>
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365 </data>
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366
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367 <data format="fastq" name="output_suppressed_reads_r"
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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368 label="${tool.name} on ${on_string}: suppressed reads (R)">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
369 <filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
370 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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371 singlePaired['sPaired'] == "paired" and
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372 params['settingsType'] == "custom" and
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373 params['suppressed_read_file'] is True
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374 ))
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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375 </filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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376 <actions>
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377 <conditional name="singlePaired.sPaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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378 <when value="single">
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379 <action type="format">
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380 <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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381 </action>
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382 </when>
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383 <!--when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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384 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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385 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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386 </action>
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387 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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388 </conditional>
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389 </actions>
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390 </data>
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391
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392 <!-- Outout unmapped reads -->
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393 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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394 <filter>
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395 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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396 params['settingsType'] == "custom" and
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397 params['unmapped_read_file'] is True
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398 ))
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399 </filter>
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400 <actions>
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401 <conditional name="singlePaired.sPaired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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402 <when value="single">
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diff changeset
403 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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404 <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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405 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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406 </when>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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407 <!--when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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408 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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409 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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diff changeset
410 </action>
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411 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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412 </conditional>
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413 </actions>
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414 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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415 <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
416 <filter>
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417 ((
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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418 singlePaired['sPaired'] == "paired" and
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419 params['settingsType'] == "custom" and
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420 params['unmapped_read_file'] is True
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421 ))
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bgruening
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422 </filter>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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423 <actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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424 <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
425 <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
426 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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427 <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
428 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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429 </when>
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430 <!--when value="paired">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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431 <action type="format">
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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432 <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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433 </action>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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434 </when-->
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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435 </conditional>
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436 </actions>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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437 </data>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
438 </outputs>
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439 <tests>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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440 <test>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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441 <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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442 <param name="own_file" value="mm10.tiny.fa.gz" />
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443 <param name="sPaired" value="single"/>
30
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diff changeset
444 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
25
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445 <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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446 <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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447 <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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448 <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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449 <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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450 <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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451
32
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diff changeset
452 <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="94">
25
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453 <assert_contents>
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454 <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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455 <has_text text="44115" />
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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456 <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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457 <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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458 <has_text text="Bismark run complete" />
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459 </assert_contents>
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diff changeset
460 </output>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
461 <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
bgruening
parents:
diff changeset
462 <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
bgruening
parents:
diff changeset
463 </test>
30
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
464 <test>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
465 <param name="genomeSource" value="history"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
466 <param name="own_file" value="mm10.tiny.fa.gz" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
467 <param name="sPaired" value="single"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
468 <param name="input_singles" value="input1.fq" ftype="fastqsanger"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
469 <param name="sort_bam" value="false"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
470 <param name="settingsType" value="custom"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
471 <param name="suppressed_read_file" value="true"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
472 <param name="unmapped_read_file" value="true"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
473 <param name="bismark_stdout" value="true"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
474 <param name="isReportOutput" value="true"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
475
32
c5003e3c507d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents: 31
diff changeset
476 <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="94">
30
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
477 <assert_contents>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
478 <has_text text="Sequences analysed in total:" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
479 <has_text text="1000" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
480 <has_text text="Mapping efficiency:" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
481 <has_text text="0.8%" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
482 <has_text text="Bismark run complete" />
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
483 </assert_contents>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
484 </output>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
485 <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
486 <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
50c594522ed2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
bgruening
parents: 28
diff changeset
487 </test>
31
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
488 <test>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
489 <param name="genomeSource" value="history"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
490 <param name="own_file" value="mm10.tiny.fa.gz" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
491 <param name="sPaired" value="paired"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
492 <repeat name="mate_list">
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
493 <param name="input_mate1" value="input1.fq" ftype="fastqsanger"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
494 <param name="input_mate2" value="input1.fq" ftype="fastqsanger"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
495 </repeat>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
496 <param name="sort_bam" value="false"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
497 <param name="settingsType" value="custom"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
498 <param name="suppressed_read_file" value="true"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
499 <param name="unmapped_read_file" value="true"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
500 <param name="bismark_stdout" value="true"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
501 <param name="isReportOutput" value="true"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
502
32
c5003e3c507d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567
bgruening
parents: 31
diff changeset
503 <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="94">
31
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
504 <assert_contents>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
505 <has_text text="Sequence pairs analysed in total:" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
506 <has_text text="1000" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
507 <has_text text="Mapping efficiency:" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
508 <has_text text="0.0%" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
509 <has_text text="Bismark run complete" />
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
510 </assert_contents>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
511 </output>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
512 <output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
513 <output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
45b1a9520fa9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents: 30
diff changeset
514 </test>
33
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
515 <test>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
516 <param name="genomeSource" value="history"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
517 <param name="own_file" value="mm10.tiny.fa.gz" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
518 <param name="sPaired" value="single"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
519 <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
520 <param name="sort_bam" value="false"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
521 <param name="settingsType" value="custom"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
522 <param name="suppressed_read_file" value="true"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
523 <param name="unmapped_read_file" value="true"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
524 <param name="bismark_stdout" value="true"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
525 <param name="isReportOutput" value="true"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
526 <conditional name="params">
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
527 <param name="settingsType" value="custom" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
528 <param name="score_min" value="L,0,-0.8" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
529 </conditional>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
530
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
531 <output name="output_stdout" file="summary_custom.txt" ftype="txt" lines_diff="94">
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
532 <assert_contents>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
533 <has_text text="Sequences analysed in total:" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
534 <has_text text="44115" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
535 <has_text text="Mapping efficiency:" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
536 <has_text text="4.5%" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
537 <has_text text="Bismark run complete" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
538 </assert_contents>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
539 </output>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
540 <output name="report_file" file="mapping_report_custom.txt" ftype="txt" lines_diff="6"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
541 <output name="output" file="mapped_reads_custom.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
542
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
543 <assert_command>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
544 <has_text text="--score-min 'L,0,-0.8'" />
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
545 </assert_command>
f06523fe7828 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
bgruening
parents: 32
diff changeset
546 </test>
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
547 </tests>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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548
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549 <help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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550 <![CDATA[
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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551
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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552 **What it does**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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553
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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554 | Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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555 | 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).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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556 | 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).
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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557 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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558 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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559 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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560 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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561 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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562
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563 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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564
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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565 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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diff changeset
566
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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567 **Know what you are doing**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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568
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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569 .. class:: warningmark
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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570
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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571 | There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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572 | In other words = running this tool with default parameters will probably not give you meaningful results.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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573 | A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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574 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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575
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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576 .. class:: warningmark
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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577
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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578 | 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.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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579
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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580 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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581
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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582 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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583
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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584 **Input formats**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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585
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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586 | 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
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587
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588 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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589
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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590 **A Note on Built-in Reference Genomes**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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591
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592 | 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
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593 | 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
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594 | The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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595
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596 ----
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597
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598 **Outputs**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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599
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600 * The final output of Bismark is in SAM format by default, and has the following columns::
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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601
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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602 Column Description
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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603 -------- --------------------------------------------------------
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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604 1 QNAME seq-ID
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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605 2 FLAG this flag tries to take the strand a bisulfite read
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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606 originated from into account
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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607 (this is different from ordinary DNA alignment flags!)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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608 3 RNAME chromosome
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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609 4 POS start position
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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610 5 MAPQ always 255
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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611 6 CIGAR extended CIGAR string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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612 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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613 8 MPOS 1-based Mate POSition
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614 9 ISIZE Inferred insert SIZE
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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615 10 SEQ query SEQuence on the same strand as the reference
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616 11 QUAL Phred33 scale
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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617 12 NM-tag edit distance to the reference)
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618 13 XX-tag base-by-base mismatches to the reference.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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619 This does not include indels.
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620 14 XM-tag methylation call string
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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621 15 XR-tag read conversion state for the alignment
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622 16 XG-tag genome conversion state for the alignment
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623
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624
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625 | Each read of paired-end alignments is written out in a separate line in the above format.
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626 |
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627
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628 * It looks like this (scroll sideways to see the entire example)::
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629
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630 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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631 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
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632 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
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633
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634 ----
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635
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636 **Note on Bismark settings**
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637
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638 | 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
bgruening
parents:
diff changeset
639
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
640 ----
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
641
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
642 **Bismark settings**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
643
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
644 * **If Paired-End Reads**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
645
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
646 * **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
647
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
648 | 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
649 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
650 | Alignment option *-I/--minins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
651
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
652
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
653 * **Maximum 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
654
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
655 | 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
656 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
657 | Alignment option *-X/--maxins <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
658
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
659
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
660 * **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
bgruening
parents:
diff changeset
661
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
662 | 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
bgruening
parents:
diff changeset
663 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
664 | Bowtie 2 Specific option *-N <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
665
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
666 * **Length of the seed substrings to align during multiseed alignment**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
667
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
668 | 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
669 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
670 | 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
671
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
672
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
673 * **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
bgruening
parents:
diff changeset
674
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
675 | Up to <int> consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using the alignments found so far. A seed extension "fails" if it does not yield a new best or a new second-best alignment. Default: 15.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
676 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
677 | Bowtie 2 Effort option *-D <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
678
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
679 * **Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
680
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
681 | <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default: 2.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
682 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
683 | Bowtie 2 Effort option *-R <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
684
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
685 * **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
bgruening
parents:
diff changeset
686
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
687 | Only aligns the first <int> reads or read pairs from the input. Default: no limit.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
688 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
689 | Input option *-u/--upto <INT>*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
690
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
691 * **Skip (i.e. do not align) the first N reads or read pairs from the input**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
692
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
693 | Input option *-s/--skip*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
694
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
695 * **Disable looking for discordant alignments if it cannot find any concordant alignments**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
696
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
697 | Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior and it is on by default.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
698 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
699 | Bowtie 2 Paired-End option *--no-discordant*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
700
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
701 * **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
bgruening
parents:
diff changeset
702
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
703 | This option disables Bowtie 2's behavior to try to find alignments for the individual mates if it cannot find a concordant or discordant alignment for a pair. This option is invariable and on by default.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
704 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
705 | Bowtie 2 Paired-End option *--no-mixed*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
706
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
707 * **Write ambiguous reads to an extra output file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
708
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
709 | Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely to a file in the output directory. Written reads will appear as they did in the input, without any of the translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
710 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
711 | Output option *--ambiguous*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
712
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
713 * **Write all reads that could not be aligned to a file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
714
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
715 | Write all reads that could not be aligned to a file in the output directory. Written reads will appear as they did in the input, without any translation of quality values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping) are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
716 |
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
717 | Output option *-un/--unmapped*
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
718
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
719 * **Offer all report files concatenated in one file**
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
720
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
721 | Prints out a Bismark mapping report
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
722
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
723 ]]>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
724 </help>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
725 <citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
726 <citation type="doi">10.1093/bioinformatics/btr167</citation>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
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727 </citations>
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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728 </tool>