Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 2:a60283899c6d draft
Version 0.32.2: use GALAXY_SLOTS to set number of threads.
| author | pjbriggs |
|---|---|
| date | Wed, 22 Apr 2015 09:36:27 -0400 |
| parents | 2bd7cdbb6228 |
| children | f8a9a5eaca8a |
| rev | line source |
|---|---|
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Version 0.32.2: use GALAXY_SLOTS to set number of threads.
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1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.2"> |
| 0 | 2 <description>flexible read trimming tool for Illumina NGS data</description> |
| 3 <command interpreter="bash">trimmomatic.sh | |
| 4 -mx8G | |
| 5 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar | |
| 6 #if $paired_end.is_paired_end | |
|
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Version 0.32.2: use GALAXY_SLOTS to set number of threads.
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7 PE -threads \${GALAXY_SLOTS:-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 |
| 0 | 8 #else |
|
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Version 0.32.2: use GALAXY_SLOTS to set number of threads.
pjbriggs
parents:
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changeset
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9 SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out |
| 0 | 10 #end if |
| 11 ## ILLUMINACLIP option | |
| 12 #if $illuminaclip.do_illuminaclip | |
| 13 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold | |
| 14 #end if | |
| 15 ## Other operations | |
| 16 #for $op in $operations | |
| 17 ## SLIDINGWINDOW | |
| 18 #if str( $op.operation.name ) == "SLIDINGWINDOW" | |
| 19 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality | |
| 20 #end if | |
| 21 ## MINLEN:36 | |
| 22 #if str( $op.operation.name ) == "MINLEN" | |
| 23 MINLEN:$op.operation.minlen | |
| 24 #end if | |
| 25 #if str( $op.operation.name ) == "LEADING" | |
| 26 LEADING:$op.operation.leading | |
| 27 #end if | |
| 28 #if str( $op.operation.name ) == "TRAILING" | |
| 29 TRAILING:$op.operation.trailing | |
| 30 #end if | |
| 31 #if str( $op.operation.name ) == "CROP" | |
| 32 CROP:$op.operation.crop | |
| 33 #end if | |
| 34 #if str( $op.operation.name ) == "HEADCROP" | |
| 35 HEADCROP:$op.operation.headcrop | |
| 36 #end if | |
| 37 #end for | |
| 38 </command> | |
| 39 <requirements> | |
| 40 <requirement type="package" version="0.32">trimmomatic</requirement> | |
| 41 </requirements> | |
| 42 <inputs> | |
| 43 <conditional name="paired_end"> | |
| 44 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> | |
| 45 <when value="no"> | |
| 46 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> | |
| 47 </when> | |
| 48 <when value="yes"> | |
| 49 <param name="fastq_r1_in" type="data" format="fastqsanger" | |
| 50 label="Input FASTQ file (R1/first of pair)" /> | |
| 51 <param name="fastq_r2_in" type="data" format="fastqsanger" | |
| 52 label="Input FASTQ file (R2/second of pair)" /> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 <conditional name="illuminaclip"> | |
| 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" /> | |
| 57 <when value="yes"> | |
| 58 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
| 59 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
| 60 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
| 61 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
| 62 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
| 63 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
| 64 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
| 65 </param> | |
| 66 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> | |
| 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" /> | |
| 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" /> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
| 72 <conditional name="operation"> | |
| 73 <param name="name" type="select" label="Select Trimmomatic operation to perform"> | |
| 74 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
| 75 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
| 76 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
| 77 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
| 78 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
| 79 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
| 80 </param> | |
| 81 <when value="SLIDINGWINDOW"> | |
| 82 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
| 83 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
| 84 </when> | |
| 85 <when value="MINLEN"> | |
| 86 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
| 87 </when> | |
| 88 <when value="LEADING"> | |
| 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" /> | |
| 90 </when> | |
| 91 <when value="TRAILING"> | |
| 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" /> | |
| 93 </when> | |
| 94 <when value="CROP"> | |
| 95 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
| 96 </when> | |
| 97 <when value="HEADCROP"> | |
| 98 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
| 99 </when> | |
| 100 </conditional> | |
| 101 </repeat> | |
| 102 </inputs> | |
| 103 <outputs> | |
| 104 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${on_string} (R1 paired)"> | |
| 105 <filter>paired_end['is_paired_end']</filter> | |
| 106 </data> | |
| 107 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${on_string} (R1 unpaired)"> | |
| 108 <filter>paired_end['is_paired_end']</filter> | |
| 109 </data> | |
| 110 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${on_string} (R2 paired)"> | |
| 111 <filter>paired_end['is_paired_end']</filter> | |
| 112 </data> | |
| 113 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${on_string} (R2 unpaired)"> | |
| 114 <filter>paired_end['is_paired_end']</filter> | |
| 115 </data> | |
| 116 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${on_string}"> | |
| 117 <filter>not paired_end['is_paired_end']</filter> | |
| 118 </data> | |
| 119 </outputs> | |
| 120 <tests> | |
| 121 <test> | |
| 122 <!-- Single-end example --> | |
| 123 <param name="is_paired_end" value="no" /> | |
| 124 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 125 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 126 <!-- | |
| 127 **NB** outputs have to be specified in order that they appear in the | |
| 128 tool (which is the order they will be written to the history) - the | |
| 129 test framework seems to use the order and ignores the "name" attribute | |
| 130 --> | |
| 131 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
| 132 </test> | |
| 133 <test> | |
| 134 <!-- Paired-end example --> | |
| 135 <param name="is_paired_end" value="yes" /> | |
| 136 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 137 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 138 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 139 <!-- | |
| 140 **NB** outputs have to be specified in order that they appear in the | |
| 141 tool (which is the order they will be written to the history) - the | |
| 142 test framework seems to use the order and ignores the "name" attribute | |
| 143 --> | |
| 144 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
| 145 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 146 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 147 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 148 </test> | |
| 149 <test> | |
| 150 <!-- Single-end example (cropping) --> | |
| 151 <param name="is_paired_end" value="no" /> | |
| 152 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 153 <param name="operations_0|operation|name" value="CROP" /> | |
| 154 <param name="operations_0|operation|crop" value="10" /> | |
| 155 <!-- | |
| 156 **NB** outputs have to be specified in order that they appear in the | |
| 157 tool (which is the order they will be written to the history) - the | |
| 158 test framework seems to use the order and ignores the "name" attribute | |
| 159 --> | |
| 160 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> | |
| 161 </test> | |
| 162 </tests> | |
| 163 <help> | |
| 164 .. class:: infomark | |
| 165 | |
| 166 **What it does** | |
| 167 | |
| 168 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
| 169 single ended data. | |
| 170 | |
| 171 This tool allows the following trimming steps to be performed: | |
| 172 | |
| 173 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
| 174 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average | |
| 175 quality within the window falls below a threshold | |
| 176 * **MINLEN:** Drop the read if it is below a specified length | |
| 177 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
| 178 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
| 179 * **CROP:** Cut the read to a specified length | |
| 180 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
| 181 | |
| 182 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
| 183 can be mixed and matched and will be performed in the order that they have been | |
| 184 specified. | |
| 185 | |
| 186 .. class:: warningmark | |
| 187 | |
| 188 Note that trimming operation order is important. | |
| 189 | |
| 190 ------------- | |
| 191 | |
| 192 .. class:: infomark | |
| 193 | |
| 194 **Outputs** | |
| 195 | |
| 196 For paired-end data a particular strength of Trimmomatic is that it retains the | |
| 197 pairing of reads (from R1 and R2) in the filtered output files: | |
| 198 | |
| 199 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
| 200 both have survived filtering. | |
| 201 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
| 202 one of the pair failed the filtering steps. | |
| 203 | |
| 204 Retaining the same order and number of reads in the filtered output fastq files is | |
| 205 essential for many downstream analysis tools. | |
| 206 | |
| 207 For single-end data the output is a single FASTQ file containing just the filtered | |
| 208 reads. | |
| 209 | |
| 210 ------------- | |
| 211 | |
| 212 .. class:: infomark | |
| 213 | |
| 214 **Credits** | |
| 215 | |
| 216 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
| 217 University of Manchester. It runs the Trimmomatic program which has been developed | |
| 218 within Bjorn Usadel's group at RWTH Aachen university. | |
| 219 | |
| 220 Trimmomatic website (including documentation): | |
| 221 | |
| 222 * http://www.usadellab.org/cms/index.php?page=trimmomatic | |
| 223 | |
| 224 The reference for Trimmomatic is: | |
| 225 | |
| 1 | 226 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer |
| 227 for Illumina Sequence Data. Bioinformatics, btu170. | |
| 0 | 228 |
| 229 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
| 230 use it. | |
| 231 </help> | |
| 1 | 232 <citations> |
| 233 <!-- | |
| 234 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 235 Can be either DOI or Bibtex | |
| 236 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 237 --> | |
| 238 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
| 239 </citations> | |
| 0 | 240 </tool> |