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1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.1">
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2 <description>flexible read trimming tool for Illumina NGS data</description>
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3 <command interpreter="bash">trimmomatic.sh
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4 -mx8G
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5 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
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6 #if $paired_end.is_paired_end
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7 PE -threads 6 -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired
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8 #else
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9 SE -threads 6 -phred33 $fastq_in $fastq_out
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10 #end if
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11 ## ILLUMINACLIP option
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12 #if $illuminaclip.do_illuminaclip
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13 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
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14 #end if
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15 ## Other operations
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16 #for $op in $operations
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17 ## SLIDINGWINDOW
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18 #if str( $op.operation.name ) == "SLIDINGWINDOW"
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19 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
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20 #end if
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21 ## MINLEN:36
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22 #if str( $op.operation.name ) == "MINLEN"
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23 MINLEN:$op.operation.minlen
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24 #end if
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25 #if str( $op.operation.name ) == "LEADING"
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26 LEADING:$op.operation.leading
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27 #end if
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28 #if str( $op.operation.name ) == "TRAILING"
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29 TRAILING:$op.operation.trailing
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30 #end if
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31 #if str( $op.operation.name ) == "CROP"
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32 CROP:$op.operation.crop
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33 #end if
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34 #if str( $op.operation.name ) == "HEADCROP"
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35 HEADCROP:$op.operation.headcrop
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36 #end if
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37 #end for
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38 </command>
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39 <requirements>
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40 <requirement type="package" version="0.32">trimmomatic</requirement>
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41 </requirements>
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42 <inputs>
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43 <conditional name="paired_end">
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44 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
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45 <when value="no">
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46 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />
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47 </when>
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48 <when value="yes">
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49 <param name="fastq_r1_in" type="data" format="fastqsanger"
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50 label="Input FASTQ file (R1/first of pair)" />
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51 <param name="fastq_r2_in" type="data" format="fastqsanger"
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52 label="Input FASTQ file (R2/second of pair)" />
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53 </when>
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54 </conditional>
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55 <conditional name="illuminaclip">
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56 <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="off" />
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57 <when value="yes">
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58 <param name="adapter_fasta" type="select" label="Adapter sequences to use">
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59 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
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60 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
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61 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
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62 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
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63 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
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64 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
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65 </param>
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66 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
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67 <param name="palindrome_clip_threshold" type="integer" label="How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment" value="30" />
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68 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
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69 </when>
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70 </conditional>
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71 <repeat name="operations" title="Trimmomatic Operation" min="1">
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72 <conditional name="operation">
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73 <param name="name" type="select" label="Select Trimmomatic operation to perform">
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74 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
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75 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
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76 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
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77 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
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78 <option value="CROP">Cut the read to a specified length (CROP)</option>
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79 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
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80 </param>
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81 <when value="SLIDINGWINDOW">
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82 <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
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83 <param name="required_quality" type="integer" label="Average quality required" value="20" />
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84 </when>
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85 <when value="MINLEN">
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86 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
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87 </when>
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88 <when value="LEADING">
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89 <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
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90 </when>
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91 <when value="TRAILING">
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92 <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
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93 </when>
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94 <when value="CROP">
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95 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
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96 </when>
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97 <when value="HEADCROP">
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98 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
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99 </when>
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100 </conditional>
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101 </repeat>
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102 </inputs>
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103 <outputs>
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104 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${on_string} (R1 paired)">
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105 <filter>paired_end['is_paired_end']</filter>
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106 </data>
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107 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${on_string} (R1 unpaired)">
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108 <filter>paired_end['is_paired_end']</filter>
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109 </data>
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110 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${on_string} (R2 paired)">
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111 <filter>paired_end['is_paired_end']</filter>
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112 </data>
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113 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${on_string} (R2 unpaired)">
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114 <filter>paired_end['is_paired_end']</filter>
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115 </data>
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116 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${on_string}">
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117 <filter>not paired_end['is_paired_end']</filter>
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118 </data>
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119 </outputs>
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120 <tests>
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121 <test>
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122 <!-- Single-end example -->
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123 <param name="is_paired_end" value="no" />
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124 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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125 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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126 <!--
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127 **NB** outputs have to be specified in order that they appear in the
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128 tool (which is the order they will be written to the history) - the
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129 test framework seems to use the order and ignores the "name" attribute
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130 -->
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131 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
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132 </test>
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133 <test>
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134 <!-- Paired-end example -->
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135 <param name="is_paired_end" value="yes" />
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136 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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137 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
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138 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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139 <!--
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140 **NB** outputs have to be specified in order that they appear in the
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141 tool (which is the order they will be written to the history) - the
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142 test framework seems to use the order and ignores the "name" attribute
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143 -->
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144 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
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145 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
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146 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
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147 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
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148 </test>
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149 <test>
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150 <!-- Single-end example (cropping) -->
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151 <param name="is_paired_end" value="no" />
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152 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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153 <param name="operations_0|operation|name" value="CROP" />
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154 <param name="operations_0|operation|crop" value="10" />
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155 <!--
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156 **NB** outputs have to be specified in order that they appear in the
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157 tool (which is the order they will be written to the history) - the
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158 test framework seems to use the order and ignores the "name" attribute
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159 -->
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160 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
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161 </test>
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162 </tests>
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163 <help>
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164 .. class:: infomark
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165
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166 **What it does**
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167
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168 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
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169 single ended data.
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170
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171 This tool allows the following trimming steps to be performed:
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172
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173 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read
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174 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average
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175 quality within the window falls below a threshold
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176 * **MINLEN:** Drop the read if it is below a specified length
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177 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
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178 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
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179 * **CROP:** Cut the read to a specified length
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180 * **HEADCROP:** Cut the specified number of bases from the start of the read
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181
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182 If ILLUMINACLIP is requested then it is always performed first; subsequent options
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183 can be mixed and matched and will be performed in the order that they have been
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184 specified.
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185
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186 .. class:: warningmark
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187
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188 Note that trimming operation order is important.
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189
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190 -------------
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191
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192 .. class:: infomark
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193
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194 **Outputs**
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195
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196 For paired-end data a particular strength of Trimmomatic is that it retains the
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197 pairing of reads (from R1 and R2) in the filtered output files:
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198
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199 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
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200 both have survived filtering.
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201 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
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202 one of the pair failed the filtering steps.
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203
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204 Retaining the same order and number of reads in the filtered output fastq files is
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205 essential for many downstream analysis tools.
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206
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207 For single-end data the output is a single FASTQ file containing just the filtered
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208 reads.
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209
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210 -------------
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211
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212 .. class:: infomark
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213
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214 **Credits**
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215
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216 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
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217 University of Manchester. It runs the Trimmomatic program which has been developed
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218 within Bjorn Usadel's group at RWTH Aachen university.
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219
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220 Trimmomatic website (including documentation):
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221
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222 * http://www.usadellab.org/cms/index.php?page=trimmomatic
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223
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224 The reference for Trimmomatic is:
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225
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226 * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a
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227 user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
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228 Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7)
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229
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230 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
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231 use it.
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232 </help>
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233 </tool>
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