annotate trim_galore.xml @ 9:1bfc7254232e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
author bgruening
date Thu, 16 Mar 2017 13:48:46 -0400
parents f1e71aeaa923
children b4e39d993fc8
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1 <tool id="trim_galore" name="Trim Galore!" version="0.4.2">
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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]*$</validator>
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21 </param>
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22 <yield/>
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23 </when>
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24 </conditional>
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25 </macro>
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26 <macro name="paired_adapter_trimming">
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28 <expand macro="adapter_trimming">
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29 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
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30 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</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 ## trim_galore removes .fastq and .fq file extensions of input files.
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58 ## This is essential if Galaxy provides links to files (with real extensions)
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59 ## but that behaviour is causing an inconsistency in output filenaming.
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60 ## We work around this by linking every file to cwd without file extension
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61
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62 #if $singlePaired.sPaired == "single":
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63 #if str($singlePaired.input_singles).endswith(".gz"):
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64 ln -s "${singlePaired.input_singles}" ./input_singles.gz;
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65 #else
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66 ln -s "${singlePaired.input_singles}" ./input_singles;
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67 #end if
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68 #elif $singlePaired.sPaired == "paired":
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69 #if str($singlePaired.input_mate1).endswith(".gz"):
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70 ln -s "${singlePaired.input_mate1}" ./input_mate1.gz;
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71 ln -s "${singlePaired.input_mate2}" ./input_mate2.gz;
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72 #else
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73 ln -s "${singlePaired.input_mate1}" ./input_mate1;
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74 ln -s "${singlePaired.input_mate2}" ./input_mate2;
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75 #end if
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76 #else:
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77 #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):
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78 ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1.gz;
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79 ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2.gz;
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80 #else
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81 ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;
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82 ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;
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83 #end if
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84 #end if
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85
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86 perl $__tool_directory__/trim_galore
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87
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88 ## we only support fastqsanger
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89 --phred33
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90
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91 #if $params.settingsType == "custom":
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92
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93 ## default 20
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94 --quality $params.quality
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95
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96 ## default 1
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97 --stringency $params.stringency
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98
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99 ## default 0.1
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100 -e $params.error_rate
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101
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102 ## default 20
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103 --length $params.min_length
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104
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105 #if $params.clip_R1:
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106 --clip_R1 $params.clip_R1
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107 #end if
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108
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109 #if $params.clip_R2:
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110 --clip_R2 $params.clip_R2
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111 #end if
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112
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113 #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output":
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114 --retain_unpaired
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115 --length_1 $params.retain_unpaired.length_1
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116 --length_2 $params.retain_unpaired.length_2
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117 #end if
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118
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119 #end if
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120
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121 ## RBBS specific options.
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122 #if $rrbs.settingsType == "custom":
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123 $rrbs.rrbs
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124 $rrbs.non_directional
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125 #end if
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126
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127 --output_dir ./
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128 --suppress_warn
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129
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130 #if $params.settingsType == "custom" and not $params.report:
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131 --no_report_file
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132 #end if
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133
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134 #if $singlePaired.trimming.trimming_select == 'user':
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135 ## default 'AGATCGGAAGAGC'
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136 #if $singlePaired.trimming.adapter.strip() != '':
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137 --adapter $singlePaired.trimming.adapter
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138 #end if
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139 #else:
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140 $singlePaired.trimming.trimming_select
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141 #end if
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142
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143
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144 #if $singlePaired.three_prime_clip_R1:
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145 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
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146 #end if
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147
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148 #if $singlePaired.sPaired == "single":
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149 ## input sequence
8
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150 #if str($singlePaired.input_singles).endswith(".gz"):
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151 ./input_singles.gz
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152 --dont_gzip
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153 #else
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154 ./input_singles
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155 #end if
6
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156 #else:
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157 --paired
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158
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159 $singlePaired.trim1
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160
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161 #if $singlePaired.trimming.trimming_select == 'user':
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162 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
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163 --adapter2 $singlePaired.trimming.adapter2
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164 #end if
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165 #end if
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166
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167 #if $singlePaired.three_prime_clip_R2:
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168 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
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169 #end if
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170
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171 ## input sequences
8
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172 #if $singlePaired.sPaired == "paired":
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173 #if str($singlePaired.input_mate1).endswith(".gz"):
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174 ./input_mate1.gz
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175 ./input_mate2.gz
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176 --dont_gzip
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177 #else
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178 ./input_mate1
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179 ./input_mate2
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180 #end if
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181 #else:
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182 #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):
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183 ./input_mate1.gz
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184 ./input_mate2.gz
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185 --dont_gzip
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186 #else
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187 ./input_mate1
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188 ./input_mate2
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189 #end if
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190 #end if
6
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191
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192 #end if
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193
8
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194 ## Trim Galore is finished, rename the output if compressed
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195 &&
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196 if [ -f input_singles.gz_trimmed.fq ] ; then mv input_singles.gz_trimmed.fq input_singles_trimmed.fq ; fi
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197 &&
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198 if [ -f input_mate1.gz_val_1.fq ] ; then mv input_mate1.gz_val_1.fq input_mate1_val_1.fq ; fi
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199 &&
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200 if [ -f input_mate2.gz_val_2.fq ] ; then mv input_mate2.gz_val_2.fq input_mate2_val_2.fq ; fi
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201 &&
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202 if [ -f input_mate1.gz_unpaired_1.fq ] ; then mv input_mate1.gz_unpaired_1.fq input_mate1_unpaired_1.fq ; fi
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203 &&
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204 if [ -f input_mate2.gz_unpaired_2.fq ] ; then mv input_mate2.gz_unpaired_2.fq input_mate2_unpaired_2.fq ; fi
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205
6
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206 ## Trim Galore! run is finished. Move the report files to the proper place
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207 #if $params.settingsType == "custom" and $params.report:
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208 &&
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209 cat ./*_trimming_report.txt > $report_file;
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210 #end if
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211
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212 ]]>
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213 </command>
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214 <inputs>
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215 <!-- Input Parameters -->
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216 <conditional name="singlePaired">
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217 <param name="sPaired" type="select" label="Is this library paired- or single-end?">
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218 <option value="single">Single-end</option>
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219 <option value="paired">Paired-end</option>
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220 <option value="paired_collection">Paired Collection</option>
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221 </param>
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222 <when value="single">
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223 <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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224 <expand macro="adapter_trimming"/>
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225
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226 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
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227 <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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228 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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229 (--three_prime_clip_R1)</help>
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230 </param>
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231 </when>
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232 <when value="paired">
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233 <param name="input_mate1" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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234 <param name="input_mate2" type="data" format="fastqsanger" label="Reads in FASTQ format" />
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235 <expand macro="paired_adapter_trimming" />
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236 </when>
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237 <when value="paired_collection">
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238 <param name="input_mate_pairs" format="fastqsanger" type="data_collection" collection_type="paired"
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239 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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240 <expand macro="paired_adapter_trimming" />
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241 </when>
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242 </conditional>
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243
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244 <conditional name="params">
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245 <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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246 <option value="default">Use defaults</option>
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247 <option value="custom">Full parameter list</option>
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248 </param>
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249 <when value="default" />
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250 <!-- Full/advanced params. -->
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251 <when value="custom">
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252 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)"
6
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253 help="For more information please see below." />
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254 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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255 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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256 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />
6
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257
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258 <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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259 <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)" />
6
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260
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261 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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262
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263 <conditional name="retain_unpaired">
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264 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
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265 <option value="no_output">Do not output unpaired reads</option>
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266 <option value="retain_unpaired_output">Output unpaired reads</option>
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267 </param>
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268 <when value="no_output" />
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269 <!-- Output params. -->
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270 <when value="retain_unpaired_output">
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271 <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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272 <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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273 </when> <!-- output -->
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274 </conditional> <!-- retain_unpaired -->
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275
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276 </when> <!-- full -->
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277 </conditional> <!-- params -->
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278
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279 <conditional name="rrbs">
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280 <param name="settingsType" type="select" label="RRBS specific settings">
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281 <option value="default">Use defaults (no RRBS)</option>
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282 <option value="custom">Full parameter list</option>
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283 </param>
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284 <when value="default" />
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285 <!-- Full/advanced params. -->
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286 <when value="custom">
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287 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
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288 label="Specifies that the input file was an MspI digested RRBS sample" />
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289 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
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290 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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291 </when> <!-- full -->
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292 </conditional> <!-- params -->
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293
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294 </inputs>
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295 <outputs>
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296 <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
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297 <filter>singlePaired['sPaired'] == "single"</filter>
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298 </data>
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299
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300 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
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301 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" />
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302 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" />
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303 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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304 </collection>
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305
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306 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
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307 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" />
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308 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" />
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309 <filter>params['settingsType'] == "custom"</filter>
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310 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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311 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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312 </collection>
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313
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314 <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq"
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315 label="${tool.name} on ${on_string}: trimmed reads pair 1">
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316 <filter>singlePaired['sPaired'] == "paired"</filter>
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317 </data>
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318
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319 <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
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320 label="${tool.name} on ${on_string}: trimmed reads pair 2">
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321 <filter>singlePaired['sPaired'] == "paired"</filter>
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322 </data>
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323
7
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324 <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
6
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325 label="${tool.name} on ${on_string}: unpaired reads (1)">
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326 <filter>params['settingsType'] == "custom"</filter>
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327 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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328 <filter>singlePaired['sPaired'] == "paired"</filter>
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329 </data>
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330
7
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331 <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
6
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332 label="${tool.name} on ${on_string}: unpaired reads (2)">
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333 <filter>params['settingsType'] == "custom"</filter>
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334 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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335 <filter>singlePaired['sPaired'] == "paired"</filter>
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336 </data>
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337 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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338 <filter>params['settingsType'] == "custom"</filter>
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339 <filter>params['report'] == True</filter>
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340 </data>
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341
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342 </outputs>
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343 <tests>
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344 <test>
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345 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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346 <param name="sPaired" value="single" />
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347 <param name="settingsType" value="custom" />
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348 <param name="report" value="true" />
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349 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
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350 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" />
6
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351 </test>
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352
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353 <test>
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354 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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355 <param name="sPaired" value="single" />
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356 <param name="trimming_select" value="--illumina" />
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357 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
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358 </test>
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359
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360 <test>
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361 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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362 <param name="sPaired" value="single" />
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363 <param name="adapter" value="AAAGAGC" />
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364 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
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365 </test>
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366
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367 <test>
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368 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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369 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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370 <param name="sPaired" value="paired" />
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371 <param name="settingsType" value="custom" />
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372 <param name="report" value="true" />
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373 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
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374 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
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375 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
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376 </test>
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377
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378 <test>
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379 <param name="input_mate_pairs">
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380 <collection type="paired">
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381 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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382 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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383 </collection>
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384 </param>
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385
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386 <param name="sPaired" value="paired_collection" />
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387 <param name="settingsType" value="custom" />
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388 <param name="report" value="true" />
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389 <param name="retain_unpaired_select" value="retain_unpaired_output" />
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390
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391 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
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392
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393 <output_collection name="trimmed_reads_paired_collection" type="paired">
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394 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
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395 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
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396 </output_collection>
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397
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398 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
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399 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
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400 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
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401 </output_collection>
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402
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403 </test>
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404 </tests>
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405 <help>
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406 <![CDATA[
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407 **What it does**
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408
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409 `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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410
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411 * 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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412 * 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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413 * 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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414 * The Phred quality of basecalls and the stringency for adapter removal can be specified individually
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415 * 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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416 * 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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417
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418 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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419
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420 It is developed by Felix Krueger at the Babraham Institute.
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421
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422 ----
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423
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424 **Main Settings**
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425
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426 * **Adapter sequence to be trimmed**
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427
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428 * **Automatic detection**
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429
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430 | 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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431
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432 * **Illumina universal**
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433
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434 | 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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435 |
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436 | *option --illumina*
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437
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438 * **Nextera transposase**
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439
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440 | 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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441 |
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442 | *option --nextera*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
443
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
444 * **Illumina small RNA adapters**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
445
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
446 | 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.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
447 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
448 | *option --small_rna*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
449
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
450 * **User defined adapter trimming**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
451
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
452 | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence.
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
453 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
454 | *option -a*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
455
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
456 * **If Single-End Reads**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
457
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
458 * **Remove <int> bp from the 3' end**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
459
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
460 | <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
461 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
462 | *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
463
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
464 * **If Paired-End Reads**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
465
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
466 * **Trims 1 bp off every read from its 3' end**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
467
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
468 | 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:
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
469 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
470 | R1 --------------------------->
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
471 | R2 <---------------------------
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
472 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
473 | or this:
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
474 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
475 | R1 ----------------------->
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
476 | R2 <-----------------
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
477 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
478 | 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
479 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
480 | *option --t*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
481
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
482 * **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
483
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
484 | <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
485 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
486 | *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
487
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
488 * **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
489
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
490 | <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
491 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
492 | *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
493
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
494 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
495
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
496 **Advanced Settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
497
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
498 * **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
499
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
500 | 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
501 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
502 | *option -q*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
503
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
504 * **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
505
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
506 | 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
507 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
508 | *option -s*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
509
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
510 * **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
511
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
512 | (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
513 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
514 | *option -e*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
515
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
516 * **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
517
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
518 | 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
519 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
520 | 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
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diff changeset
521 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
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diff changeset
522 | *option --length*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
523
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
524 * **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
525
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
526 | 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
527 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
528 | *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
529
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
bgruening
parents: 8
diff changeset
530 * **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
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531
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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532 | 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
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533 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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534 | *option --clip_R2*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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535
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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536 * **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
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537
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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538 | 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
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539 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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540 | *option --retained_unpaired*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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541
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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542 ----
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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543
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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544 **RRBS specific settings**
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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545
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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546 * **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
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547
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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548 | 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
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549 |
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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550 | *option -rrbs*
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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551
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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552 * **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
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553
1bfc7254232e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923
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554 | 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
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555 |
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556 | *option --non_directional*]]>
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557 </help>
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558 <citations></citations>
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559 </tool>