Mercurial > repos > bgruening > trim_galore

annotate trim_galore.xml @ 16:cc01cbc4e7f7 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
author bgruening
date Fri, 08 Oct 2021 09:57:12 +0000
parents 313e04fe07cd
children
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cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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1 <tool id="trim_galore" name="Trim Galore!" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Quality and adapter trimmer of reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="xrefs"/>
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8 <version_command>
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9 trim_galore --version
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10 </version_command>
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11 <command detect_errors="aggressive"><![CDATA[
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12 #set compressed = 'no'
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13 #if $singlePaired.sPaired == "single":
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14 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
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15 #set read1 = 'input_1.fastq.gz'
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16 #set compressed = 'gz'
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17 #else
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18 #set read1 = 'input_1.fastq'
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19 #end if
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20 ln -s '${singlePaired.input_singles}' ${read1} &&
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21 #elif $singlePaired.sPaired == "paired":
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22 #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
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23 #set read1 = 'input_1.fastq.gz'
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24 #set compressed = 'gz'
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25 #else
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26 #set read1 = 'input_1.fastq'
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27 #end if
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28 ln -s '${singlePaired.input_mate1}' ${read1} &&
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30 #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
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31 #set read2 = 'input_2.fastq.gz'
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32 #else
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33 #set read2 = 'input_2.fastq'
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34 #end if
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35 ln -s '${singlePaired.input_mate2}' ${read2} &&
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36 #else:
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37 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
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38 #set read1 = 'input_1.fastq.gz'
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39 #set compressed = 'gz'
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40 #else
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41 #set read1 = 'input_1.fastq'
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42 #end if
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43 ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} &&
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45 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
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46 #set read2 = 'input_2.fastq.gz'
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47 #else
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48 #set read2 = 'input_2.fastq'
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49 #end if
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50 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
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51 #end if
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52
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53 trim_galore
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54
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55 ## according the develpers 4 cores could be a sweet spot, anything above has diminishing returns
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56 --cores \${GALAXY_SLOTS:-4}
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57
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58 ## we only support fastqsanger
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59 --phred33
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61 #if $params.settingsType == "custom":
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62
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63 ## default 20
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64 --quality $params.quality
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65
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66 ## default 1
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67 --stringency $params.stringency
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68
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69 ## default 0.1
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70 -e $params.error_rate
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72 ## default 20
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73 --length $params.min_length
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75 #if $params.clip_R1:
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76 --clip_R1 $params.clip_R1
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77 #end if
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79 #if $params.clip_R2:
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80 --clip_R2 $params.clip_R2
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81 #end if
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82
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83 #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output":
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84 --retain_unpaired
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85 --length_1 $params.retain_unpaired.length_1
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86 --length_2 $params.retain_unpaired.length_2
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87 #end if
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88
4
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89 #end if
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90
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91 ## RBBS specific options.
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92 #if $rrbs.settingsType == "custom":
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93 $rrbs.rrbs
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94 $rrbs.non_directional
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95 #end if
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96
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97 --output_dir ./
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98
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99 #if $params.settingsType == "custom" and not $params.report:
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100 --no_report_file
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101 #end if
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102
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103 #if $singlePaired.trimming.trimming_select == 'user':
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104 ## default 'AGATCGGAAGAGC'
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105 #if $singlePaired.trimming.adapter.strip() != '':
11
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106 --adapter '$singlePaired.trimming.adapter'
4
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107 #end if
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108 #else:
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109 $singlePaired.trimming.trimming_select
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110 #end if
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111
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112 #if $singlePaired.three_prime_clip_R1:
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113 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
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114 #end if
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115
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116 #if $singlePaired.sPaired == "single":
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117 ## input sequence
10
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118 ${read1}
4
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119 #else:
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120 --paired
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121
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122 $singlePaired.trim1
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123
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124 #if $singlePaired.trimming.trimming_select == 'user':
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125 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
11
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126 --adapter2 '$singlePaired.trimming.adapter2'
4
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127 #end if
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128 #end if
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129
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130 #if $singlePaired.three_prime_clip_R2:
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131 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
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132 #end if
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133
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134 ## input sequences
10
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135 ${read1}
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136 ${read2}
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137 #end if
4
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138
10
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139 #if $compressed == 'no':
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140 --dont_gzip
4
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141 #end if
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142
16
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143 ## Trimming settings
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144 #if $trimming.settingsType == 'custom'
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145 #if $trimming.hardtrim5
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146 --hardtrim5 $trimming.hardtrim5
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147 #end if
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148 #if $trimming.hardtrim3
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149 --hardtrim3 $trimming.hardtrim3
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150 #end if
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151 $trimming.clock
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152 $trimming.polyA
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153 #end if
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154
6
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155 ## Trim Galore is finished, rename the output if compressed
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156 &&
10
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157 if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi
6
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158 &&
10
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159 if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi
6
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160 &&
10
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161 if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi
6
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162 &&
10
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163 if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi
6
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164 &&
10
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165 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
16
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166 &&
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167 if [ -f input_1.clock_UMI.R1.fq.gz ] ; then mv input_1.clock_UMI.R1.fq.gz input_1.clock_UMI.R1.fq ; fi
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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168 &&
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169 if [ -f input_2.clock_UMI.R2.fq.gz ] ; then mv input_2.clock_UMI.R2.fq.gz input_2.clock_UMI.R2.fq ; fi
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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170
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171 ## Rename hardtrimmed files
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172 #if $trimming.settingsType == 'custom'
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173 &&
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174 if [ -f input_1.${trimming.hardtrim5}bp_5prime.fq.gz ] ; then mv input_1.${trimming.hardtrim5}bp_5prime.fq.gz input_1_hardtrim.fq ; fi
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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175 &&
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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176 if [ -f input_2.${trimming.hardtrim5}bp_5prime.fq.gz ] ; then mv input_2.${trimming.hardtrim5}bp_5prime.fq.gz input_2_hardtrim.fq ; fi
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177 &&
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178 if [ -f input_1.${trimming.hardtrim3}bp_3prime.fq.gz ] ; then mv input_1.${trimming.hardtrim3}bp_3prime.fq.gz input_1_hardtrim.fq ; fi
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179 &&
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180 if [ -f input_2.${trimming.hardtrim3}bp_3prime.fq.gz ] ; then mv input_2.${trimming.hardtrim3}bp_3prime.fq.gz input_2_hardtrim.fq ; fi
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181 &&
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182 if [ -f input_1.${trimming.hardtrim5}bp_5prime.fq ] ; then mv input_1.${trimming.hardtrim5}bp_5prime.fq input_1_hardtrim.fq ; fi
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183 &&
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184 if [ -f input_2.${trimming.hardtrim5}bp_5prime.fq ] ; then mv input_2.${trimming.hardtrim5}bp_5prime.fq input_2_hardtrim.fq ; fi
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185 &&
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186 if [ -f input_1.${trimming.hardtrim3}bp_3prime.fq ] ; then mv input_1.${trimming.hardtrim3}bp_3prime.fq input_1_hardtrim.fq ; fi
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187 &&
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188 if [ -f input_2.${trimming.hardtrim3}bp_3prime.fq ] ; then mv input_2.${trimming.hardtrim3}bp_3prime.fq input_2_hardtrim.fq ; fi
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189 #end if
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190
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191 ## Trim Galore! run is finished. Move the report files to the proper place
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192 #if $params.settingsType == "custom" and $params.report:
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193 &&
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194 cat ./*_trimming_report.txt > '$report_file'
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195 #end if
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196 && ls -lah
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197 ]]></command>
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198 <inputs>
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199 <!-- Input Parameters -->
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200 <conditional name="singlePaired">
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201 <param name="sPaired" type="select" label="Is this library paired- or single-end?">
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202 <option value="single">Single-end</option>
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203 <option value="paired">Paired-end</option>
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204 <option value="paired_collection">Paired Collection</option>
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205 </param>
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206 <when value="single">
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207 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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208 <expand macro="adapter_trimming"/>
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209
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210 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
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211 <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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212 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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213 (--three_prime_clip_R1)</help>
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214 </param>
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215 </when>
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216 <when value="paired">
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217 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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218 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
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219 <expand macro="paired_adapter_trimming" />
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220 </when>
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221 <when value="paired_collection">
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222 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
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223 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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224 <expand macro="paired_adapter_trimming" />
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225 </when>
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226 </conditional>
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227
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228 <conditional name="params">
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229 <param name="settingsType" type="select" label="Advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
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230 <option value="default">Use defaults</option>
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231 <option value="custom">Full parameter list</option>
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232 </param>
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233 <when value="default" />
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234 <!-- Full/advanced params. -->
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235 <when value="custom">
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236 <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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237 help="For more information please see below." />
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238 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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239 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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240 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />
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241
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242 <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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243 <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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244
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245 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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246
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247 <conditional name="retain_unpaired">
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248 <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads">
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249 <option value="no_output">Do not output unpaired reads</option>
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250 <option value="retain_unpaired_output">Output unpaired reads</option>
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251 </param>
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252 <when value="no_output" />
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253 <!-- Output params. -->
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254 <when value="retain_unpaired_output">
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255 <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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256 <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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257 </when> <!-- output -->
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258 </conditional> <!-- retain_unpaired -->
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259
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260 </when> <!-- full -->
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261 </conditional> <!-- params -->
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262
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263 <conditional name="rrbs">
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264 <param name="settingsType" type="select" label="RRBS specific settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
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265 <option value="default">Use defaults (no RRBS)</option>
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266 <option value="custom">Full parameter list</option>
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267 </param>
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268 <when value="default" />
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269 <!-- Full/advanced params. -->
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270 <when value="custom">
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271 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True"
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272 label="Specifies that the input file was an MspI digested RRBS sample" />
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273 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False"
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274 label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
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275 </when> <!-- full -->
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276 </conditional> <!-- params -->
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277 <!--Trimming options-->
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278 <conditional name="trimming">
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279 <param name="settingsType" type="select" label="Trimming settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
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280 <option value="default">Use defaults</option>
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281 <option value="custom">Full parameter list</option>
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282 </param>
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283 <when value="default" />
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284 <when value="custom">
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285 <param argument="--hardtrim5" type="integer" min="1" optional="true" label="Hard-trimm 5' ends" help="Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 5'-end. Once hard-trimming of files is complete, it will exit" />
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286 <param argument="--hardtrim3" type="integer" min="1" optional="true" label="Hard-trimm 3' ends" help="Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 3'-end. Once hard-trimming of files is complete, it will exit" />
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287 <param argument="--clock" type="boolean" truevalue="--clock" falsevalue="" label="Mouse epigenetic clock mode" help="In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock"/>
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288 <param argument="--polyA" type="boolean" truevalue="--polyA" falsevalue="" label="Remove polyA tails" help="This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences" />
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289 </when>
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290 </conditional>
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291 </inputs>
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292
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293 <outputs>
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294 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
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295 <filter>singlePaired['sPaired'] == "single"</filter>
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296 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
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297 </data>
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298
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299 <data format_source="input_singles" name="hardtrim_reads_single" from_work_dir="input_1_hardtrim.fq" label="${tool.name} on ${on_string}: hard-trimmed reads">
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300 <filter>singlePaired['sPaired'] == "single"</filter>
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301 <filter>trimming['settingsType'] == "custom"</filter>
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302 <filter>trimming['hardtrim3'] != '' or trimming['hardtrim5'] != ''</filter>
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303 </data>
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304
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305 <!--Trimmed reads paired collection-->
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306 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
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307 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" />
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308 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" />
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309 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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310 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
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311 <filter>trimming['clock'] == False</filter>
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312 </collection>
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313
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314 <!--Unpaired reads collection-->
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315 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
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316 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" />
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317 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_unpaired_2.fq" />
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318 <filter>params['settingsType'] == "custom"</filter>
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319 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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320 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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321 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
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322 </collection>
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323
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324 <!--Hard-trimmed reads paired collection-->
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325 <collection name="hardtrimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: hard-trimmed paired reads">
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326 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_hardtrim.fq" />
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327 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_hardtrim.fq" />
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328 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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329 <filter>trimming['settingsType'] == "custom"</filter>
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330 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
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331 </collection>
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332
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333 <!--Mouse epigenetic reads paired collection-->
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334 <collection name="mouse_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: MEC paired reads">
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335 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1.clock_UMI.R1.fq" />
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336 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2.clock_UMI.R2.fq" />
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337 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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338 <filter>trimming['settingsType'] == "custom"</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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339 <filter>trimming['clock']</filter>
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340 </collection>
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341
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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342
10
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343 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
4
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344 label="${tool.name} on ${on_string}: trimmed reads pair 1">
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345 <filter>singlePaired['sPaired'] == "paired"</filter>
16
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346 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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347 <filter>trimming['clock'] == False</filter>
4
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348 </data>
9
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349
10
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350 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
4
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351 label="${tool.name} on ${on_string}: trimmed reads pair 2">
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352 <filter>singlePaired['sPaired'] == "paired"</filter>
16
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353 <filter>trimming['hardtrim3'] == '' and trimming['hardtrim5'] == ''</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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354 <filter>trimming['clock'] == False</filter>
4
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355 </data>
9
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356
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357 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
4
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358 label="${tool.name} on ${on_string}: unpaired reads (1)">
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359 <filter>params['settingsType'] == "custom"</filter>
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360 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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361 <filter>singlePaired['sPaired'] == "paired"</filter>
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362 </data>
9
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363
10
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364 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
4
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diff changeset
365 label="${tool.name} on ${on_string}: unpaired reads (2)">
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366 <filter>params['settingsType'] == "custom"</filter>
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367 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
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368 <filter>singlePaired['sPaired'] == "paired"</filter>
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369 </data>
16
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370 <!--Hard-trimmed paired reads-->
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371 <data format_source="input_mate1" name="hardtrimmed_reads_pair1" from_work_dir="input_1_hardtrim.fq"
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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372 label="${tool.name} on ${on_string}: hard-trimmed reads pair 1">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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373 <filter>singlePaired['sPaired'] == "paired"</filter>
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374 <filter>trimming['settingsType'] == 'custom'</filter>
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375 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
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bgruening
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diff changeset
376 </data>
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377
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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378 <data format_source="input_mate2" name="hardtrimmed_reads_pair2" from_work_dir="input_2_hardtrim.fq"
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
379 label="${tool.name} on ${on_string}: hard-trimmed reads pair 2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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380 <filter>singlePaired['sPaired'] == "paired"</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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381 <filter>trimming['settingsType'] == 'custom'</filter>
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382 <filter>trimming['hardtrim3'] or trimming['hardtrim5']</filter>
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bgruening
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diff changeset
383 </data>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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384
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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385 <!--Mouse epigenetic mode paired reads-->
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386 <data format_source="input_mate1" name="mec_reads_pair1" from_work_dir="input_1.clock_UMI.R1.fq"
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
387 label="${tool.name} on ${on_string}: MEC reads pair 1">
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388 <filter>singlePaired['sPaired'] == "paired"</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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389 <filter>trimming['settingsType'] == 'custom'</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
390 <filter>trimming['clock']</filter>
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391 </data>
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diff changeset
392
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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393 <data format_source="input_mate2" name="mec_reads_pair2" from_work_dir="input_2.clock_UMI.R2.fq"
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
394 label="${tool.name} on ${on_string}: MEC reads pair 2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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395 <filter>singlePaired['sPaired'] == "paired"</filter>
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396 <filter>trimming['settingsType'] == 'custom'</filter>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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397 <filter>trimming['clock']</filter>
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398 </data>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
399
4
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400 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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diff changeset
401 <filter>params['settingsType'] == "custom"</filter>
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402 <filter>params['report'] == True</filter>
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403 </data>
11
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diff changeset
404 </outputs>
9
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diff changeset
405
4
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406 <tests>
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407 <test expect_num_outputs="2">
4
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408 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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409 <param name="sPaired" value="single" />
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410 <param name="settingsType" value="custom" />
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411 <param name="report" value="true" />
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412 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
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413 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" />
4
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414 </test>
16
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415 <test expect_num_outputs="2">
10
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diff changeset
416 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
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417 <param name="sPaired" value="single" />
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418 <param name="settingsType" value="custom" />
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419 <param name="report" value="true" />
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diff changeset
420 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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diff changeset
421 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" />
10
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bgruening
parents: 9
diff changeset
422 </test>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
423
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
424 <test expect_num_outputs="1">
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
425 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
426 <param name="sPaired" value="single" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
427 <param name="trimming_select" value="--illumina" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
428 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
429 </test>
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
430 <test expect_num_outputs="1">
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
431 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
432 <param name="sPaired" value="single" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
433 <param name="trimming_select" value="--illumina" />
14
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parents: 13
diff changeset
434 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
10
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bgruening
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diff changeset
435 </test>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
436
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
437 <test expect_num_outputs="1">
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
438 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
439 <param name="sPaired" value="single" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
440 <param name="adapter" value="AAAGAGC" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
441 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
442 </test>
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cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
443 <test expect_num_outputs="1">
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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parents: 9
diff changeset
444 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
445 <param name="sPaired" value="single" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
446 <param name="adapter" value="AAAGAGC" />
14
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parents: 13
diff changeset
447 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
10
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bgruening
parents: 9
diff changeset
448 </test>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
449
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cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
450 <test expect_num_outputs="3">
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
451 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
452 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
453 <param name="sPaired" value="paired" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
454 <param name="settingsType" value="custom" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
455 <param name="report" value="true" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
456 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
457 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
6
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diff changeset
458 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
4
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diff changeset
459 </test>
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
460 <test expect_num_outputs="3">
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
461 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
462 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
463 <param name="sPaired" value="paired" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
464 <param name="settingsType" value="custom" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
465 <param name="report" value="true" />
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bgruening
parents: 13
diff changeset
466 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
773202ae55c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
parents: 13
diff changeset
467 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
468 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
469 </test>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
470
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
471 <test expect_num_outputs="7">
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
472 <param name="input_mate_pairs">
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
473 <collection type="paired">
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
474 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
475 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
476 </collection>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
477 </param>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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parents:
diff changeset
478
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
479 <param name="sPaired" value="paired_collection" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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parents:
diff changeset
480 <param name="settingsType" value="custom" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
481 <param name="report" value="true" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
482 <param name="retain_unpaired_select" value="retain_unpaired_output" />
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
483
6
864b3b2d32dd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit d48f42b1c267c8ebfc50161ea764baed8ee66701-dirty
bgruening
parents: 5
diff changeset
484 <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" />
4
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diff changeset
485
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
486 <output_collection name="trimmed_reads_paired_collection" type="paired">
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
487 <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
488 <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
489 </output_collection>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
490
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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491 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
492 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
493 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
494 </output_collection>
10
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diff changeset
495 </test>
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
496 <test expect_num_outputs="7">
10
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diff changeset
497 <param name="input_mate_pairs">
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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parents: 9
diff changeset
498 <collection type="paired">
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
499 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
500 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
501 </collection>
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
502 </param>
4
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diff changeset
503
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
504 <param name="sPaired" value="paired_collection" />
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diff changeset
505 <param name="settingsType" value="custom" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
506 <param name="report" value="true" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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507 <param name="retain_unpaired_select" value="retain_unpaired_output" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
508
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
509 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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510
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
511 <output_collection name="trimmed_reads_paired_collection" type="paired">
14
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512 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
773202ae55c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
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diff changeset
513 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
514 </output_collection>
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
515
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
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diff changeset
516 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
14
773202ae55c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
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diff changeset
517 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
773202ae55c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5
bgruening
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diff changeset
518 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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diff changeset
519 </output_collection>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
520 </test>
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
521 <!--Test hard-trim option-->
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
522 <test expect_num_outputs="2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
523 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
524 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
525 <param name="sPaired" value="paired" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
526 <conditional name="trimming">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
527 <param name="settingsType" value="custom" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
528 <param name="hardtrim3" value="20"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
529 </conditional>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
530 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair1_.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
531 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed3_pair2_.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
532 </test>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
533 <test expect_num_outputs="2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
534 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
535 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
536 <param name="sPaired" value="paired" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
537 <conditional name="trimming">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
538 <param name="settingsType" value="custom" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
539 <param name="hardtrim5" value="20"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
540 </conditional>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
541 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair1_.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
542 <output name="hardtrimmed_reads_pair1" file="paired_hardtrimmed5_pair2_.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
543 </test>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
544
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
545 <!--Test mouse epigenetic clock option-->
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
546 <test expect_num_outputs="2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
547 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
548 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
549 <param name="sPaired" value="paired" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
550 <conditional name="trimming">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
551 <param name="settingsType" value="custom" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
552 <param name="clock" value="true"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
553 </conditional>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
554 <output name="mec_reads_pair1" file="mec_reads_pair1.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
555 <output name="mec_reads_pair2" file="mec_reads_pair2.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
556 </test>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
557 <!--Test polyA option-->
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
558 <test expect_num_outputs="2">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
559 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
560 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
561 <param name="sPaired" value="paired" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
562 <conditional name="trimming">
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
563 <param name="settingsType" value="custom" />
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
564 <param name="polyA" value="true"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
565 </conditional>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
566 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair1.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
567 <output name="trimmed_reads_pair1" file="trimmed_polyA_reads_pair2.fastqsanger" ftype="fastqsanger"/>
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
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diff changeset
568 </test>
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
569 </tests>
11
09219a47e3a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
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diff changeset
570 <help><![CDATA[
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
571 **What it does**
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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parents:
diff changeset
572
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
573 `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:
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
574
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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diff changeset
575 * 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
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
576 * 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
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
577 * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
578 * The Phred quality of basecalls and the stringency for adapter removal can be specified individually
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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parents:
diff changeset
579 * 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
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
580 * 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
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
581
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
diff changeset
582
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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diff changeset
583 It is developed by Felix Krueger at the Babraham Institute.
9
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
584
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
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diff changeset
585 ----
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
586
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
587 **Main Settings**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
588
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
589 * **Adapter sequence to be trimmed**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
590
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
591 * **Automatic detection**
11
09219a47e3a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
592
9
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
593 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
594
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
595 * **Illumina universal**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
596
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
597 | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
598 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
599 | *option --illumina*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
600
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
601 * **Nextera transposase**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
602
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
603 | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
604 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
605 | *option --nextera*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
606
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
607 * **Illumina small RNA adapters**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
608
10
02efbf4740c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
bgruening
parents: 9
diff changeset
609 | 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
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
610 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
611 | *option --small_rna*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
612
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
613 * **User defined adapter trimming**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
614
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
615 | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
616 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
617 | *option -a*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
618
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
619 * **If Single-End Reads**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
620
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
621 * **Remove <int> bp from the 3' end**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
622
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
623 | <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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
624 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
625 | *option --three_prime_clip_R1*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
626
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
627 * **If Paired-End Reads**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
628
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
629 * **Trims 1 bp off every read from its 3' end**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
630
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
631 | 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:
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
632 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
633 | R1 --------------------------->
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
634 | R2 <---------------------------
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
635 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
636 | or this:
11
09219a47e3a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
637 |
9
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
638 | R1 ----------------------->
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
639 | R2 <-----------------
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
640 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
641 | as invalid (whenever a start/end coordinate is contained within the other read).
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
642 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
643 | *option --t*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
644
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
645 * **Remove <int> bp from the 3' end of read 1**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
646
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
647 | <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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
648 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
649 | *option --three_prime_clip_R1*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
650
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
651 * **Remove <int> bp from the 3' end of read 2**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
652
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
653 | <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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
654 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
655 | *option --three_prime_clip_R2*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
656
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
657 ----
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
658
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
659 **Advanced Settings**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
660
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
661 * **Trim low-quality ends from reads in addition to adapter removal**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
662
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
663 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
664 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
665 | *option -q*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
666
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
667 * **Overlap with adapter sequence required to trim a sequence**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
668
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
669 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
670 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
671 | *option -s*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
672
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
673 * **Maximum allowed error rate**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
674
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
675 | (no. of errors divided by the length of the matching region) (default: 0.1).
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
676 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
677 | *option -e*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
678
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
679 * **Discard reads that became shorter than length <INT>**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
680
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
681 | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
682 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
683 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
684 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
685 | *option --length*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
686
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
687 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 1**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
688
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
689 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
690 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
691 | *option --clip_R1*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
692
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
693 * **Instructs Trim Galore! to remove INT bp from the 5' end of read 2**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
694
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
695 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
696 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
697 | *option --clip_R2*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
698
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
699 * **Specify if you would like to retain unpaired reads**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
700
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
701 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
702 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
703 | *option --retained_unpaired*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
704
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
705 ----
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
706
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
707 **RRBS specific settings**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
708
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
709 * **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
710
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
711 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
712 |
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
713 | *option -rrbs*
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
714
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
715 * **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
716
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
717 | 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.
383e9f2eaa6c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
bgruening
parents: 8
diff changeset
718 |
11
09219a47e3a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
diff changeset
719 | *option --non_directional*
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
720
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
721 ----
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
722
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
723 **Trim specific seetings**
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
724
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
725 * **Hard-trimming mode**
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
726
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
727 | Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to N bp at the 5' or 3' -end.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
728 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
729 | *options -hardtrim5 and -hardtrim3*
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
730
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
731 * **Mouse Epigenetic Clock mode**
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
732
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
733 | In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock (see here: `Multi-tissue DNA methylation age predictor in mouse`_). Following this, Trim Galore will exit.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
734 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
735 | In it's current implementation, the dual-UMI RRBS reads come in the following format:
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
736 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
737 | Read 1 5' UUUUUUUU CAGTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF TACTG UUUUUUUU 3'
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
738 | Read 2 3' UUUUUUUU GTCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF ATGAC UUUUUUUU 5'
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
739 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
740 | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI), CAGTA is a constant region, and FFFFFFF... is the actual RRBS-Fragment to be sequenced. The UMIs for Read 1 (R1) and Read 2 (R2), as well as the fixed sequences (F1 or F2), are written into the read ID and removed from the actual sequence.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
741 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
742 | *option --clock*
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
743
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
744 * **PolyA mode**
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
745
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
746 | This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences. When selected, Trim Galore attempts to identify from the first supplied sample whether sequences contain more often a stretch of either 'AAAAAAAAAA' or 'TTTTTTTTTT'. This determines if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary base from the start of the reads.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
747 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
748 | PLEASE NOTE: The poly-A trimming mode expects that sequences were both adapter and quality trimmed before looking for Poly-A tails, and it is the user's responsibility to carry out an initial round of trimming.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
749 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
750 | *option --polyA*
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
751
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
752 * **Amplicon mode**
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
753
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
754 | This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads. Following this, Trim Galore will exit.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
755 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
756 | In it's current implementation, the UMI carrying reads come in the following format:
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
757 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
758 | Read 1 5' FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 3'
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
759 | Read 2 3' UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5'
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
760 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
761 | Where UUUUUUUU is a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual fragment to be sequenced.
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
762 |
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
763 | *option --amplicon*
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
764
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
765 .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
766 .. _Multi-tissue DNA methylation age predictor in mouse: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1203-5
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
767
11
09219a47e3a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
bgruening
parents: 10
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768 ]]></help>
16
cc01cbc4e7f7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
bgruening
parents: 15
diff changeset
769 <expand macro="citations" />
4
e929fb5cf477 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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770 </tool>