Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic.xml @ 16:9a38087e3bfd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
author iuc
date Sun, 14 Jan 2024 11:00:33 +0000
parents 32f1f56bd970
children b9aaed85cbd1
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1 <tool id="trimmomatic" name="Trimmomatic" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>flexible read trimming tool for Illumina NGS data</description>
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3 <macros>
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4 <import>trimmomatic_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">trimmomatic</requirement>
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8 <!--
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9 Coreutils required for 'readlink -e' work across platforms
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10 See similar fix for snpSift
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11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
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12 -->
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9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
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13 <requirement type="package" version="9.4">coreutils</requirement>
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14 </requirements>
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15 <command detect_errors="aggressive"><![CDATA[
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16 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
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17 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
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18 #if $readtype.single_or_paired == "pair_of_files"
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19 #set r1_ext = $readtype.fastq_r1_in.extension
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20 #set r2_ext = $readtype.fastq_r2_in.extension
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21 ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
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22 ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
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23 #elif $readtype.single_or_paired == "collection"
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24 #set r1_ext = $readtype.fastq_pair.forward.extension
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25 #set r2_ext = $readtype.fastq_pair.reverse.extension
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26 ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
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27 ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
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28 #else
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29 ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
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30 #end if
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31 java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
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32 #if $readtype.single_or_paired in ["pair_of_files","collection"]
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33 PE -threads \${GALAXY_SLOTS:-6}
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34 fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
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35 fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
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36 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
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37 #else
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38 SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
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39 #end if
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40 ## ILLUMINACLIP option
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9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
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41 #if $illuminaclip.do_illuminaclip == "yes"
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42 #if $illuminaclip.adapter_type.standard_or_custom == "custom"
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43 #if $readtype.single_or_paired in ["pair_of_files","collection"]
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44 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
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45 #else
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46 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
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47 #end if
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48 #else
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49 #if $readtype.single_or_paired in ["pair_of_files","collection"]
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50 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
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51 #else
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52 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
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53 #end if
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54 #end if
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55 #end if
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56 ## Other operations
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57 #for $op in $operations
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58 ## SLIDINGWINDOW
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59 #if str( $op.operation.name ) == "SLIDINGWINDOW"
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60 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
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61 #end if
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62 ## MINLEN:36
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63 #if str( $op.operation.name ) == "MINLEN"
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64 MINLEN:$op.operation.minlen
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65 #end if
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66 #if str( $op.operation.name ) == "LEADING"
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67 LEADING:$op.operation.leading
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68 #end if
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69 #if str( $op.operation.name ) == "TRAILING"
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70 TRAILING:$op.operation.trailing
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71 #end if
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72 #if str( $op.operation.name ) == "CROP"
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73 CROP:$op.operation.crop
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74 #end if
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75 #if str( $op.operation.name ) == "HEADCROP"
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76 HEADCROP:$op.operation.headcrop
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77 #end if
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78 #if str( $op.operation.name ) == "AVGQUAL"
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79 AVGQUAL:$op.operation.avgqual
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80 #end if
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81 #if str( $op.operation.name ) == "MAXINFO"
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82 MAXINFO:$op.operation.target_length:$op.operation.strictness
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83 #end if
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84 #end for
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85 #if $output_logs:
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86 -trimlog trimlog
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87 #end if
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88 #if $quality_score
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89 $quality_score
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90 #end if
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91 2>&1 | tee trimmomatic.log &&
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92 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
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93 &&
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94 #if $readtype.single_or_paired == "pair_of_files"
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95 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
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96 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
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97 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
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98 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
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99 #elif $readtype.single_or_paired == "collection"
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100 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
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101 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
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102 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
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103 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
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104 #else
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105 mv fastq_out.'$fastq_in.extension' '${fastq_out}'
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106 #end if
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107 ]]></command>
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108 <configfiles>
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109 <configfile name="adapter_file_from_text">#set from_text_area = ''
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110 #if str( $illuminaclip.do_illuminaclip ) == "yes" and str( $illuminaclip.adapter_type.standard_or_custom ) == "custom":
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111 #set from_text_area = $illuminaclip.adapter_type.adapter_text
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112 #end if
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113 ${from_text_area}</configfile>
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114 </configfiles>
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115
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116 <inputs>
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117 <conditional name="readtype">
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118 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
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119 <option value="se" selected="true">Single-end</option>
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120 <option value="pair_of_files">Paired-end (two separate input files)</option>
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121 <option value="collection">Paired-end (as collection)</option>
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122 </param>
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123 <when value="se">
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124 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
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125 </when>
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126 <when value="pair_of_files">
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127 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
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128 label="Input FASTQ file (R1/first of pair)" />
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129 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
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130 label="Input FASTQ file (R2/second of pair)" />
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131 </when>
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132 <when value="collection">
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133 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
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134 </when>
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135 </conditional>
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136 <conditional name="illuminaclip">
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137 <param name="do_illuminaclip" type="select" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read">
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138 <option value="no" selected="true">no</option>
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139 <option value="yes">yes</option>
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140 </param>
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141 <when value="yes">
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142 <conditional name="adapter_type">
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143 <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?">
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144 <option value="standard" selected="true">Standard</option>
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145 <option value="custom">Custom</option>
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146 </param>
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147 <when value="standard">
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148 <param name="adapter_fasta" type="select" label="Adapter sequences to use">
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149 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
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150 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
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151 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
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152 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
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153 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
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154 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
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155 </param>
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156 </when>
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157 <when value="custom">
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158 <param name="adapter_text" type="text" area="True" size="10x30" value=""
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159 label="Custom adapter sequences in fasta format" help="Write sequences in the fasta format.">
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160 <sanitizer>
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161 <valid initial="string.printable"></valid>
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162 <mapping initial="none"/>
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163 </sanitizer>
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164 </param>
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165 </when>
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166 </conditional>
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167 <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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168 <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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169 <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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170 <param name="min_adapter_len" type="integer" label="Minimum length of adapter that needs to be detected (PE specific/palindrome mode)" value="8" />
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171 <param name="keep_both_reads" type="boolean" label="Always keep both reads (PE specific/palindrome mode)?" truevalue="true" falsevalue="false" checked="true"
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172 help="See help below"/>
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173 </when>
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174 <when value="no" /> <!-- empty clause to satisfy planemo lint -->
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175 </conditional>
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176 <repeat name="operations" title="Trimmomatic Operation" min="1">
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177 <conditional name="operation">
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178 <param name="name" type="select" label="Select Trimmomatic operation to perform">
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179 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
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180 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
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181 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
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182 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
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183 <option value="CROP">Cut the read to a specified length (CROP)</option>
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184 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
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185 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
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186 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
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187 </param>
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188 <when value="SLIDINGWINDOW">
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189 <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
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190 <param name="required_quality" type="integer" label="Average quality required" value="20" />
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191 </when>
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192 <when value="MINLEN">
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193 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
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194 </when>
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195 <when value="LEADING">
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196 <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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197 </when>
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198 <when value="TRAILING">
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199 <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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200 </when>
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201 <when value="CROP">
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202 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
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203 </when>
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204 <when value="HEADCROP">
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205 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
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206 </when>
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207 <when value="AVGQUAL">
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208 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
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209 </when>
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210 <when value="MAXINFO">
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211 <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
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212 <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
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213 </when>
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214 </conditional>
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215 </repeat>
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216 <param name="quality_score" type="select" optional="true" label="Quality score encoding" help="The phred+64 encoding works the same as the phred+33 encoding, except you add 64 to the phred score to determine the ascii code of the quality character. You will only find phred+64 encoding on older
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217 data, which was sequenced several years ago. FASTQC can be used in order to identify the encoding type.">
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218 <option value="-phred33">Phred33</option>
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219 <option value="-phred64">Phred64</option>
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220 </param>
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221 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
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222 <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
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223 </inputs>
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224 <outputs>
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225 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
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226 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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227 </data>
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228 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
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229 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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230 </data>
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231 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
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232 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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233 </data>
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234 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
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235 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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236 </data>
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237 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
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238 <filter>readtype['single_or_paired'] == 'se'</filter>
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239 </data>
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240 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
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241 <filter>readtype['single_or_paired'] == "collection"</filter>
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242 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
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243 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
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244 </collection>
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245 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
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246 <filter>readtype['single_or_paired'] == "collection"</filter>
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247 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
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248 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
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249 </collection>
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250 <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
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251 <filter>output_logs</filter>
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252 </data>
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253 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">
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254 <filter>output_err</filter>
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255 </data>
0
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256 </outputs>
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257 <tests>
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258 <test expect_num_outputs="3">
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259 <!-- Single-end example -->
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260 <conditional name="readtype">
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261 <param name="single_or_paired" value="se" />
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262 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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263 </conditional>
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264 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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265 <param name="output_logs" value="yes" />
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266 <param name="output_err" value="yes" />
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267 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
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268 <output name="log_file" file="trimmomatic_se_out1.log" />
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269 <output name="err_file" compare="re_match" file="trimmomatic_se_out1.err.re_match" />
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270 </test>
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271 <test expect_num_outputs="1">
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272 <!-- Single-end example - gzipped -->
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273 <param name="single_or_paired" value="se" />
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274 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
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275 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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276 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
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277 </test>
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278 <test expect_num_outputs="4">
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279 <!-- Paired-end example - gzipped -->
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280 <param name="single_or_paired" value="pair_of_files" />
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281 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
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282 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
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283 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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284 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
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285 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
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286 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
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287 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
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288 </test>
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289 <test expect_num_outputs="4">
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290 <!-- Paired-end example -->
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291 <param name="single_or_paired" value="pair_of_files" />
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292 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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293 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
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294 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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295 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
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296 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
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297 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
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298 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
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299 </test>
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300 <test expect_num_outputs="4">
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301 <!-- Paired-end Illumina 1.3-1.7 quality encoding -->
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302 <param name="single_or_paired" value="pair_of_files" />
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303 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" />
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304 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" />
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305 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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306 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" />
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307 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" />
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308 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" />
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309 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" />
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310 </test>
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311 <test expect_num_outputs="4">
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312 <!-- Paired-end Solexa quality encoding -->
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313 <param name="single_or_paired" value="pair_of_files" />
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314 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" />
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315 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" />
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316 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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317 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" />
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318 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" />
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319 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" />
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320 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" />
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321 </test>
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322 <test expect_num_outputs="1">
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323 <!-- Single-end example (cropping) -->
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324 <param name="single_or_paired" value="se" />
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325 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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326 <param name="operations_0|operation|name" value="CROP" />
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327 <param name="operations_0|operation|crop" value="10" />
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328 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
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329 </test>
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330 <test expect_num_outputs="6">
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331 <!-- Paired-end with dataset collection -->
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332 <param name="single_or_paired" value="collection" />
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333 <param name="fastq_pair">
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334 <collection type="paired">
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335 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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336 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
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337 </collection>
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338 </param>
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339 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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340 <output_collection name="fastq_out_paired" type="paired">
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341 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
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342 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
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343 </output_collection>
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344 <output_collection name="fastq_out_unpaired" type="paired">
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345 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
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346 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
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347 </output_collection>
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348 </test>
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349 <test expect_num_outputs="6">
6
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350 <!-- Paired-end with dataset collection - gzipped -->
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351 <param name="single_or_paired" value="collection" />
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352 <param name="fastq_pair">
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353 <collection type="paired">
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354 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
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355 <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>
141bba0e9a77 Uploaded v0.36.2 (adds support for compressed fastq inputs)
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356 </collection>
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357 </param>
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358 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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359 <output_collection name="fastq_out_paired" type="paired">
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360 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
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361 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
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362 </output_collection>
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363 <output_collection name="fastq_out_unpaired" type="paired">
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364 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
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365 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
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366 </output_collection>
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367 </test>
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368 <test expect_num_outputs="1">
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369 <!-- Single-end using AVGQUAL -->
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370 <param name="single_or_paired" value="se" />
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371 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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372 <param name="operations_0|operation|name" value="AVGQUAL" />
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373 <param name="operations_0|operation|avgqual" value="30" />
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374 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
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375 </test>
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376 <test expect_num_outputs="1">
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377 <!-- Single-end using MAXINFO -->
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378 <param name="single_or_paired" value="se" />
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379 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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380 <param name="operations_0|operation|name" value="MAXINFO" />
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381 <param name="operations_0|operation|target_length" value="75" />
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382 <param name="operations_0|operation|strictness" value="0.8" />
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383 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
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384 </test>
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385 <test expect_num_outputs="4">
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386 <!-- Paired-end ILLUMINACLIP - this does not check valid clipping -->
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387 <param name="single_or_paired" value="pair_of_files" />
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388 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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389 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
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390 <param name="do_illuminaclip" value="yes"/>
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391 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
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392 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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393 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
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394 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
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395 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
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396 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
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397 </test>
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398 <test expect_num_outputs="4">
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399 <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping -->
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400 <param name="single_or_paired" value="pair_of_files" />
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401 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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402 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
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403 <param name="do_illuminaclip" value="yes"/>
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404 <param name="standard_or_custom" value="custom"/>
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405 <param name="adapter_text"
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406 value=">PrefixPE/1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PrefixPE/2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PCR_Primer1_rc&#10;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT&#10;>PCR_Primer2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer2_rc&#10;AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG&#10;>FlowCell1&#10;TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC&#10;>FlowCell2&#10;TTTTTTTTTTCAAGCAGAAGACGGCATACGA&#10;"/>
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407 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
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408 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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409 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
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410 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
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411 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
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412 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
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413 </test>
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414 <test expect_num_outputs="3">
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415 <!-- Quality score test -->
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416 <conditional name="readtype">
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417 <param name="single_or_paired" value="se" />
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418 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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419 </conditional>
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420 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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421 <param name="output_logs" value="yes" />
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422 <param name="output_err" value="yes" />
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423 <param name="quality_score" value="-phred33"/>
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424 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
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425 <output name="log_file" file="trimmomatic_se_out1.log" />
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426 <output name="err_file" compare="re_match" file="trimmomatic_se_out2.err.re_match" />
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427 </test>
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428 </tests>
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429 <help><![CDATA[
0
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430 .. class:: infomark
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431
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432 **What it does**
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433
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434 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
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435 single ended data.
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436
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437 This tool allows the following trimming steps to be performed:
3358c3d30143 Uploaded initial version.
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438
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439 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read
8
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440
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441 * If **Always keep both reads (PE specific/palindrome mode)** is True, the reverse read will also be retained in palindrome mode.
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442 After read-though has been detected by palindrome mode, and the adapter sequence removed,
415a165d92bb Uploaded v0.36.4.
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443 the reverse read contains the same sequence information as the forward read, albeit in reverse complement.
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444 For this reason, the default behaviour is to entirely drop the reverse read.
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445 Retaining the reverse read may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads.
0
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446 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average
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447 quality within the window falls below a threshold
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448 * **MINLEN:** Drop the read if it is below a specified length
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449 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
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450 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
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451 * **CROP:** Cut the read to a specified length
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452 * **HEADCROP:** Cut the specified number of bases from the start of the read
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453 * **AVGQUAL:** Drop the read if the average quality is below a specified value
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454 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
4
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455 maximise the value of each read
0
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456
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457 If ILLUMINACLIP is requested then it is always performed first; subsequent options
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458 can be mixed and matched and will be performed in the order that they have been
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459 specified.
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460
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461 .. class:: warningmark
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462
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463 Note that trimming operation order is important.
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464
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pjbriggs
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465 -------------
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466
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pjbriggs
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467 .. class:: infomark
3358c3d30143 Uploaded initial version.
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468
3
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469 **Inputs**
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470
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471 For single-end data this Trimmomatic tool accepts a single FASTQ file; for
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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472 paired-end data it will accept either two FASTQ files (R1 and R2), or a
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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473 dataset collection containing the R1/R2 FASTQ pair.
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474
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
pjbriggs
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475 .. class:: infomark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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476
0
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477 **Outputs**
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478
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479 For paired-end data a particular strength of Trimmomatic is that it retains the
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480 pairing of reads (from R1 and R2) in the filtered output files:
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481
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482 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
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483 both have survived filtering.
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484 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
3358c3d30143 Uploaded initial version.
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485 one of the pair failed the filtering steps.
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486
3
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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487 .. class:: warningmark
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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488
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489 If the input consists of a dataset collection with the R1/R2 FASTQ pair then
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490 the outputs will also inclue two dataset collections: one for the 'paired'
f8a9a5eaca8a Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
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491 outputs and one for the 'unpaired' (as described above)
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492
0
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493 Retaining the same order and number of reads in the filtered output fastq files is
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494 essential for many downstream analysis tools.
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495
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496 For single-end data the output is a single FASTQ file containing just the filtered
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497 reads.
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498
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499 -------------
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500
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501 .. class:: infomark
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502
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503 **Credits**
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504
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505 This Galaxy tool was originally developed within the Bioinformatics Core
9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
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506 Facility at the University of Manchester, with contributions from Peter van
9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
iuc
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507 Heusden, Marius van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias
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508 Bernt and Cristóbal Gallardo. It is now maintained as part of the IUC tool
9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
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509 collection.
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510
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511 It runs the Trimmomatic program which has been developed
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512 within Bjorn Usadel's group at RWTH Aachen university.
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513
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514 Trimmomatic website (including documentation):
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515
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516 * http://www.usadellab.org/cms/index.php?page=trimmomatic
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517
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518 The reference for Trimmomatic is:
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519
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520 * Bolger, A.M., Lohse, M., &amp; Usadel, B. (2014). Trimmomatic: A flexible trimmer
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521 for Illumina Sequence Data. Bioinformatics, btu170.
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522
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523 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
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524 use it.
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525 ]]></help>
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526 <citations>
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527 <!--
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528 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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529 Can be either DOI or Bibtex
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530 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
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531 -->
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532 <citation type="doi">10.1093/bioinformatics/btu170</citation>
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533 </citations>
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534 </tool>