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annotate trim_galore.xml @ 10:b4e39d993fc8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
author bgruening
date Thu, 20 Apr 2017 09:14:30 -0400
parents 1bfc7254232e
children 80cd83b11214
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10
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1 <tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
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2 <!-- Wrapper compatible with Trim Galore! version 0.4 -->
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3 <description>Quality and adapter trimmer of reads</description>
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4 <macros>
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5 <macro name="adapter_trimming">
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6 <conditional name="trimming">
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7 <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
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8 <option value="">Automatic detection</option>
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9 <option value="--illumina">Illumina universal</option>
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10 <option value="--nextera">Nextera transposase</option>
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11 <option value="--small_rna">Illumina small RNA adapters</option>
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12 <option value="user">User defined adapter sequence</option>
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13 </param>
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14 <when value=""/>
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15 <when value="--illumina"/>
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16 <when value="--nextera"/>
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17 <when value="--small_rna"/>
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18 <when value="user">
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19 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
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20 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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21 </param>
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22 <yield/>
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23 </when>
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24 </conditional>
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25 </macro>
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26 <macro name="paired_adapter_trimming">
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27
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28 <expand macro="adapter_trimming">
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29 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
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30 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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31 </param>
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32 </expand>
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33 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
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34 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
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35 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
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36 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
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37 (--three_prime_clip_R1)</help>
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38 </param>
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39 <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
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40 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
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41 adapter/quality trimming has been performed. This may remove some unwanted bias from
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42 the 3' end that is not directly related to adapter sequence or basecall quality.</help>
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43 </param>
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44 </macro>
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45 </macros>
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46 <requirements>
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47 <!-- conda dependency -->
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48 <requirement type="package" version="1.8.3">cutadapt</requirement>
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49 <requirement type="package" version="1.8">cutadapt</requirement>
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50 </requirements>
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51 <version_command>
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52 perl '$__tool_directory__/trim_galore' --version
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53 </version_command>
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54 <command>
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55 <![CDATA[
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56
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57 #set compressed = 'no'
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58 #if $singlePaired.sPaired == "single":
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59 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
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60 #set read1 = 'input_1.fastq.gz'
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61 #set compressed = 'gz'
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62 #else
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63 #set read1 = 'input_1.fastq'
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64 #end if
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65 ln -s '${singlePaired.input_singles}' ${read1} &&
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66 #elif $singlePaired.sPaired == "paired":
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67 #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
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68 #set read1 = 'input_1.fastq.gz'
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69 #set compressed = 'gz'
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70 #else
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71 #set read1 = 'input_1.fastq'
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72 #end if
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73 ln -s '${singlePaired.input_mate1}' ${read1} &&
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74
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75 #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
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76 #set read2 = 'input_2.fastq.gz'
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77 #else
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78 #set read2 = 'input_2.fastq'
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79 #end if
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80 ln -s '${singlePaired.input_mate2}' ${read2} &&
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81 #else:
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82 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
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83 #set read1 = 'input_1.fastq.gz'
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84 #set compressed = 'gz'
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85 #else
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86 #set read1 = 'input_1.fastq'
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87 #end if
10
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88 ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} &&
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89
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90 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
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91 #set read2 = 'input_2.fastq.gz'
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92 #else
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93 #set read2 = 'input_2.fastq'
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94 #end if
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95 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
6
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96 #end if
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97
10
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98 perl '$__tool_directory__/trim_galore'
6
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99
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100 ## we only support fastqsanger
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101 --phred33
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102
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103 #if $params.settingsType == "custom":
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104
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105 ## default 20
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106 --quality $params.quality
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107
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108 ## default 1
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109 --stringency $params.stringency
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110
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111 ## default 0.1
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112 -e $params.error_rate
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113
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114 ## default 20
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115 --length $params.min_length
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116
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117 #if $params.clip_R1:
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118 --clip_R1 $params.clip_R1
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119 #end if
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120
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121 #if $params.clip_R2:
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122 --clip_R2 $params.clip_R2
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123 #end if
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124
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125 #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output":
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126 --retain_unpaired
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127 --length_1 $params.retain_unpaired.length_1
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128 --length_2 $params.retain_unpaired.length_2
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129 #end if
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130
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131 #end if
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132
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133 ## RBBS specific options.
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134 #if $rrbs.settingsType == "custom":
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135 $rrbs.rrbs
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136 $rrbs.non_directional
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137 #end if
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138
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139 --output_dir ./
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140 --suppress_warn
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141
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142 #if $params.settingsType == "custom" and not $params.report:
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143 --no_report_file
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144 #end if
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145
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146 #if $singlePaired.trimming.trimming_select == 'user':
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147 ## default 'AGATCGGAAGAGC'
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148 #if $singlePaired.trimming.adapter.strip() != '':
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149 --adapter $singlePaired.trimming.adapter
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150 #end if
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151 #else:
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152 $singlePaired.trimming.trimming_select
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153 #end if
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154
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155
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156 #if $singlePaired.three_prime_clip_R1:
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157 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
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158 #end if
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159
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160 #if $singlePaired.sPaired == "single":
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161 ## input sequence
10
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162 ${read1}
6
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163 #else:
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164 --paired
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165
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166 $singlePaired.trim1
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167
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168 #if $singlePaired.trimming.trimming_select == 'user':
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169 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
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170 --adapter2 $singlePaired.trimming.adapter2
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171 #end if
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172 #end if
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173
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174 #if $singlePaired.three_prime_clip_R2:
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175 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
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176 #end if
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177
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178 ## input sequences
10
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179 ${read1}
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180 ${read2}
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181 #end if
6
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182
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183 #if $compressed == 'no':
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184 --dont_gzip
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185 #end if
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186
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187 ## Trim Galore is finished, rename the output if compressed
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188 &&
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189 if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi
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190 &&
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191 if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi
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192 &&
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193 if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi
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194 &&
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195 if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi
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196 &&
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197 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
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198
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199 ## Trim Galore! run is finished. Move the report files to the proper place
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200 #if $params.settingsType == "custom" and $params.report:
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201 &&
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202 cat ./*_trimming_report.txt > $report_file;
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203 #end if
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204
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205 ]]>
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206 </command>
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207 <inputs>
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208 <!-- Input Parameters -->
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209 <conditional name="singlePaired">
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210 <param name="sPaired" type="select" label="Is this library paired- or single-end?">
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211 <option value="single">Single-end</option>
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212 <option value="paired">Paired-end</option>
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213 <option value="paired_collection">Paired Collection</option>
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214 </param>
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215 <when value="single">
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216 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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217 <expand macro="adapter_trimming"/>
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218
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219 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
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220 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
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221 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
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222 (--three_prime_clip_R1)</help>
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223 </param>
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224 </when>
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225 <when value="paired">
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226 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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227 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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228 <expand macro="paired_adapter_trimming" />
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229 </when>
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230 <when value="paired_collection">
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231 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
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232 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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233 <expand macro="paired_adapter_trimming" />
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234 </when>
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235 </conditional>
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236
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237 <conditional name="params">
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238 <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
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239 <option value="default">Use defaults</option>
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240 <option value="custom">Full parameter list</option>
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241 </param>
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242 <when value="default" />
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243 <!-- Full/advanced params. -->
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244 <when value="custom">
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245 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)"
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246 help="For more information please see below." />
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247 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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248 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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249 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />
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250
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251 <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 1" />
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252 <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5' end of read 2 (Only for paired-end reads)" />
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253
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254 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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255
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256 <conditional name="retain_unpaired">
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257 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
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258 <option value="no_output">Do not output unpaired reads</option>
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259 <option value="retain_unpaired_output">Output unpaired reads</option>
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260 </param>
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261 <when value="no_output" />
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262 <!-- Output params. -->
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263 <when value="retain_unpaired_output">
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264 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
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265 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
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266 </when> <!-- output -->
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267 </conditional> <!-- retain_unpaired -->
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268
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269 </when> <!-- full -->
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270 </conditional> <!-- params -->
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271
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272 <conditional name="rrbs">
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273 <param name="settingsType" type="select" label="RRBS specific settings">
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274 <option value="default">Use defaults (no RRBS)</option>
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275 <option value="custom">Full parameter list</option>
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276 </param>
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277 <when value="default" />
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278 <!-- Full/advanced params. -->
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279 <when value="custom">
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280 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
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281 label="Specifies that the input file was an MspI digested RRBS sample" />
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282 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
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283 label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
6
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284 </when> <!-- full -->
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285 </conditional> <!-- params -->
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286
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287 </inputs>
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288 <outputs>
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289 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
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290 <filter>singlePaired['sPaired'] == "single"</filter>
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291 </data>
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292
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293 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
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294 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" />
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295 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" />
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296 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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297 </collection>
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298
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299 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
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300 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" />
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301 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_unpaired_2.fq" />
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302 <filter>params['settingsType'] == "custom"</filter>
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303 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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304 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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305 </collection>
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306
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307 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
6
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308 label="${tool.name} on ${on_string}: trimmed reads pair 1">
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309 <filter>singlePaired['sPaired'] == "paired"</filter>
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310 </data>
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311
10
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312 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
6
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313 label="${tool.name} on ${on_string}: trimmed reads pair 2">
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314 <filter>singlePaired['sPaired'] == "paired"</filter>
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315 </data>
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316
10
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317 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
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318 label="${tool.name} on ${on_string}: unpaired reads (1)">
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319 <filter>params['settingsType'] == "custom"</filter>
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320 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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321 <filter>singlePaired['sPaired'] == "paired"</filter>
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322 </data>
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323
10
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324 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
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325 label="${tool.name} on ${on_string}: unpaired reads (2)">
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326 <filter>params['settingsType'] == "custom"</filter>
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327 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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328 <filter>singlePaired['sPaired'] == "paired"</filter>
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329 </data>
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330 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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331 <filter>params['settingsType'] == "custom"</filter>
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332 <filter>params['report'] == True</filter>
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333 </data>
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334
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335 </outputs>
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336 <tests>
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337 <test>
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338 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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339 <param name="sPaired" value="single" />
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340 <param name="settingsType" value="custom" />
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341 <param name="report" value="true" />
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342 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
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343 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" />
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344 </test>
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345 <test>
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346 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
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347 <param name="sPaired" value="single" />
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348 <param name="settingsType" value="custom" />
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349 <param name="report" value="true" />
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350 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
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351 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
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352 </test>
6
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353
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354 <test>
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bgruening
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diff changeset
355 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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356 <param name="sPaired" value="single" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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357 <param name="trimming_select" value="--illumina" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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358 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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359 </test>
10
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360 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
361 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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362 <param name="sPaired" value="single" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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363 <param name="trimming_select" value="--illumina" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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364 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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365 </test>
6
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366
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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367 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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368 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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369 <param name="sPaired" value="single" />
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bgruening
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370 <param name="adapter" value="AAAGAGC" />
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bgruening
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371 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
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bgruening
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372 </test>
10
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373 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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374 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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375 <param name="sPaired" value="single" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
376 <param name="adapter" value="AAAGAGC" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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377 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
378 </test>
6
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379
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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380 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
381 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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bgruening
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382 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
383 <param name="sPaired" value="paired" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
384 <param name="settingsType" value="custom" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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385 <param name="report" value="true" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
386 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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387 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
8
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bgruening
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diff changeset
388 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
6
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389 </test>
10
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diff changeset
390 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
391 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
392 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
393 <param name="sPaired" value="paired" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
394 <param name="settingsType" value="custom" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
395 <param name="report" value="true" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
396 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
397 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
398 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
399 </test>
6
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diff changeset
400
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
401 <test>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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402 <param name="input_mate_pairs">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
403 <collection type="paired">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
404 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
405 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
406 </collection>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
407 </param>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
408
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
409 <param name="sPaired" value="paired_collection" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
410 <param name="settingsType" value="custom" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
411 <param name="report" value="true" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
412 <param name="retain_unpaired_select" value="retain_unpaired_output" />
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
413
8
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diff changeset
414 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
6
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diff changeset
415
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
416 <output_collection name="trimmed_reads_paired_collection" type="paired">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
417 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
418 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
419 </output_collection>
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diff changeset
420
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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421 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
422 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
423 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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424 </output_collection>
10
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diff changeset
425 </test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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426 <test>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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427 <param name="input_mate_pairs">
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
428 <collection type="paired">
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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parents: 9
diff changeset
429 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
430 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
431 </collection>
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
432 </param>
6
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433
10
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
434 <param name="sPaired" value="paired_collection" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
435 <param name="settingsType" value="custom" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
436 <param name="report" value="true" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
437 <param name="retain_unpaired_select" value="retain_unpaired_output" />
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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438
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439 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
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440
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441 <output_collection name="trimmed_reads_paired_collection" type="paired">
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442 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
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443 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
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444 </output_collection>
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445
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446 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
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447 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
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448 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
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449 </output_collection>
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450 </test>
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451 </tests>
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452 <help>
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453 <![CDATA[
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454 **What it does**
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455
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456 `Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
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457
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458 * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
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459 * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation
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460 * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming
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461 * The Phred quality of basecalls and the stringency for adapter removal can be specified individually
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462 * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality
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463 * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1
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464
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465 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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466
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467 It is developed by Felix Krueger at the Babraham Institute.
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468
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469 ----
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470
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471 **Main Settings**
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472
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473 * **Adapter sequence to be trimmed**
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474
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475 * **Automatic detection**
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476
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477 | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.
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478
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479 * **Illumina universal**
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480
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481 | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.
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482 |
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483 | *option --illumina*
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484
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485 * **Nextera transposase**
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486
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487 | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.
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488 |
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489 | *option --nextera*
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490
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491 * **Illumina small RNA adapters**
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492
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493 | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5' adapter automatically ('GATCGTCGGACT') unless -a 2 had been defined explicitly.
9
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494 |
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495 | *option --small_rna*
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496
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497 * **User defined adapter trimming**
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498
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499 | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence.
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500 |
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501 | *option -a*
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502
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503 * **If Single-End Reads**
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504
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505 * **Remove <int> bp from the 3' end**
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506
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507 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
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508 |
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509 | *option --three_prime_clip_R1*
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510
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511 * **If Paired-End Reads**
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512
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513 * **Trims 1 bp off every read from its 3' end**
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514
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515 | This may be needed for FastQ files that are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards alignments like this:
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516 |
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517 | R1 --------------------------->
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518 | R2 <---------------------------
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519 |
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520 | or this:
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521 |
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522 | R1 ----------------------->
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523 | R2 <-----------------
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524 |
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diff changeset
525 | as invalid (whenever a start/end coordinate is contained within the other read).
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
526 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
527 | *option --t*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
528
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
529 * **Remove <int> bp from the 3' end of read 1**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
530
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
531 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
532 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
533 | *option --three_prime_clip_R1*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
534
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
535 * **Remove <int> bp from the 3' end of read 2**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
536
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
537 | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
538 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
539 | *option --three_prime_clip_R2*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
540
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
541 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
542
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
543 **Advanced Settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
544
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
545 * **Trim low-quality ends from reads in addition to adapter removal**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
546
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
547 | For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract <INT> from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
548 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
549 | *option -q*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
550
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
551 * **Overlap with adapter sequence required to trim a sequence**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
552
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
553 | Defaults to a very stringent setting of '1', i.e. even a single bp of overlapping sequence will be trimmed of the 3' end of any read.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
554 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
555 | *option -s*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
556
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
557 * **Maximum allowed error rate**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
558
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
559 | (no. of errors divided by the length of the matching region) (default: 0.1).
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
560 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
561 | *option -e*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
562
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
563 * **Discard reads that became shorter than length <INT>**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
564
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
565 | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
566 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
567 | For paired-end files, both reads of a read-pair need to be longer than <INT> bp to be printed out to validated paired-end files (see option --paired). If only one read became too short there is the possibility of keeping such unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
568 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
569 | *option --length*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
570
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
571 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 1**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
572
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
573 | Instructs Trim Galore to remove <INT> bp from the 5' end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. Default: OFF.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
574 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
575 | *option --clip_R1*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
576
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
577 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 2**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
578
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
579 | Instructs Trim Galore to remove <int> bp from the 5' end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation. Please refer to the M-bias plot section in the Bismark User Guide for some examples. Default: OFF.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
580 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
581 | *option --clip_R2*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
582
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
583 * **Specify if you would like to retain unpaired reads**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
584
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
585 | If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
586 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
587 | *option --retained_unpaired*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
588
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
589 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
590
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
591 **RRBS specific settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
592
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
593 * **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
594
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
595 | Sequences which were adapter-trimmed will have a further 2 bp removed from their 3' end. This is to avoid that the filled-in C close to the second MspI site in a sequence is used for methylation calls. Sequences which were merely trimmed because of poor quality will not be shortened further.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
596 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
597 | *option -rrbs*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
598
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
599 * **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
600
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
601 | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
602 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
603 | *option --non_directional*]]>
6
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
604 </help>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
605 <citations></citations>
11962ce40855 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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606 </tool>