Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 18:9b273be64c25 draft default tip
Updated for Trimmomatic 0.39
| author | pjbriggs |
|---|---|
| date | Thu, 02 Mar 2023 14:48:18 +0000 |
| parents | 79f875f98770 |
| children |
| rev | line source |
|---|---|
| 18 | 1 <tool id="trimmomatic" name="Trimmomatic" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 1 | 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> |
| 18 | 7 <requirement type="package" version="@TOOL_VERSION@">trimmomatic</requirement> |
| 17 | 8 <!-- |
| 9 Coreutils required for 'readlink -e' work across platforms | |
| 10 See similar fix for snpSift | |
| 11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 | |
| 16 | 12 --> |
| 13 <requirement type="package" version="8.25">coreutils</requirement> | |
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14 </requirements> |
| 7 | 15 <command detect_errors="aggressive"><![CDATA[ |
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16 @CONDA_TRIMMOMATIC_JAR_PATH@ && |
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17 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ && |
| 7 | 18 #if $readtype.single_or_paired == "pair_of_files" |
| 19 #set r1_ext = $readtype.fastq_r1_in.extension | |
| 20 #set r2_ext = $readtype.fastq_r2_in.extension | |
| 21 ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' && | |
| 22 ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' && | |
| 23 #elif $readtype.single_or_paired == "collection" | |
| 24 #set r1_ext = $readtype.fastq_pair.forward.extension | |
| 25 #set r2_ext = $readtype.fastq_pair.reverse.extension | |
| 26 ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' && | |
| 27 ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' && | |
| 28 #else | |
| 29 ln -s '$fastq_in' fastq_in.'$fastq_in.extension' && | |
| 30 #end if | |
| 31 java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar | |
| 32 #if $readtype.single_or_paired in ["pair_of_files","collection"] | |
| 12 | 33 PE -threads \${GALAXY_SLOTS:-6} |
| 7 | 34 fastq_r1.'$r1_ext' fastq_r2.'$r2_ext' |
| 35 fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext' | |
| 36 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext' | |
| 1 | 37 #else |
| 12 | 38 SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' |
| 1 | 39 #end if |
| 40 ## ILLUMINACLIP option | |
| 41 #if $illuminaclip.do_illuminaclip | |
| 9 | 42 #if $illuminaclip.adapter_type.standard_or_custom == "custom" |
| 43 #if $readtype.single_or_paired in ["pair_of_files","collection"] | |
| 44 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads | |
| 45 #else | |
| 46 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold | |
| 47 #end if | |
| 48 #else | |
| 49 #if $readtype.single_or_paired in ["pair_of_files","collection"] | |
| 50 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads | |
| 51 #else | |
| 52 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold | |
| 53 #end if | |
| 54 #end if | |
| 1 | 55 #end if |
| 56 ## Other operations | |
| 57 #for $op in $operations | |
| 58 ## SLIDINGWINDOW | |
| 59 #if str( $op.operation.name ) == "SLIDINGWINDOW" | |
| 60 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality | |
| 61 #end if | |
| 62 ## MINLEN:36 | |
| 63 #if str( $op.operation.name ) == "MINLEN" | |
| 64 MINLEN:$op.operation.minlen | |
| 65 #end if | |
| 66 #if str( $op.operation.name ) == "LEADING" | |
| 67 LEADING:$op.operation.leading | |
| 68 #end if | |
| 69 #if str( $op.operation.name ) == "TRAILING" | |
| 70 TRAILING:$op.operation.trailing | |
| 71 #end if | |
| 72 #if str( $op.operation.name ) == "CROP" | |
| 73 CROP:$op.operation.crop | |
| 74 #end if | |
| 75 #if str( $op.operation.name ) == "HEADCROP" | |
| 76 HEADCROP:$op.operation.headcrop | |
| 77 #end if | |
| 4 | 78 #if str( $op.operation.name ) == "AVGQUAL" |
| 79 AVGQUAL:$op.operation.avgqual | |
| 80 #end if | |
| 81 #if str( $op.operation.name ) == "MAXINFO" | |
| 82 MAXINFO:$op.operation.target_length:$op.operation.strictness | |
| 83 #end if | |
| 1 | 84 #end for |
| 12 | 85 #if $output_logs: |
| 86 -trimlog trimlog | |
| 87 #end if | |
| 18 | 88 #if $quality_score |
| 89 $quality_score | |
| 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 |
| 7 | 93 && |
| 94 #if $readtype.single_or_paired == "pair_of_files" | |
| 95 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' && | |
| 96 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' && | |
| 97 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' && | |
| 98 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}' | |
| 99 #elif $readtype.single_or_paired == "collection" | |
| 100 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' && | |
| 101 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' && | |
| 102 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' && | |
| 103 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}' | |
| 104 #else | |
| 105 mv fastq_out.'$fastq_in.extension' '${fastq_out}' | |
| 106 #end if | |
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107 ]]></command> |
| 9 | 108 <configfiles> |
| 109 <configfile name="adapter_file_from_text">#set from_text_area = '' | |
| 110 #if str( $illuminaclip.do_illuminaclip ) == "yes" and str( $illuminaclip.adapter_type.standard_or_custom ) == "custom": | |
| 111 #set from_text_area = $illuminaclip.adapter_type.adapter_text | |
| 112 #end if | |
| 113 ${from_text_area}</configfile> | |
| 114 </configfiles> | |
| 115 | |
| 1 | 116 <inputs> |
| 7 | 117 <conditional name="readtype"> |
| 118 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?"> | |
| 119 <option value="se" selected="true">Single-end</option> | |
| 120 <option value="pair_of_files">Paired-end (two separate input files)</option> | |
| 121 <option value="collection">Paired-end (as collection)</option> | |
| 122 </param> | |
| 123 <when value="se"> | |
| 12 | 124 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" /> |
| 1 | 125 </when> |
| 7 | 126 <when value="pair_of_files"> |
| 12 | 127 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" |
| 7 | 128 label="Input FASTQ file (R1/first of pair)" /> |
| 12 | 129 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" |
| 7 | 130 label="Input FASTQ file (R2/second of pair)" /> |
| 1 | 131 </when> |
| 7 | 132 <when value="collection"> |
| 12 | 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" /> |
| 7 | 134 </when> |
| 1 | 135 </conditional> |
| 136 <conditional name="illuminaclip"> | |
| 7 | 137 <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="False" /> |
| 138 <when value="yes"> | |
| 9 | 139 <conditional name="adapter_type"> |
| 140 <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?"> | |
| 141 <option value="standard" selected="true">Standard</option> | |
| 142 <option value="custom">Custom</option> | |
| 143 </param> | |
| 144 <when value="standard"> | |
| 145 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
| 146 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
| 147 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
| 148 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
| 149 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
| 150 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
| 151 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
| 152 </param> | |
| 153 </when> | |
| 154 <when value="custom"> | |
| 155 <param name="adapter_text" type="text" area="True" size="10x30" value="" | |
| 156 label="Custom adapter sequences in fasta format" help="Write sequences in the fasta format."> | |
| 157 <sanitizer> | |
| 158 <valid initial="string.printable"></valid> | |
| 159 <mapping initial="none"/> | |
| 160 </sanitizer> | |
| 161 </param> | |
| 162 </when> | |
| 163 </conditional> | |
| 7 | 164 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> |
| 165 <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" /> | |
| 166 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" /> | |
| 9 | 167 <param name="min_adapter_len" type="integer" label="Minimum length of adapter that needs to be detected (PE specific/palindrome mode)" value="8" /> |
| 168 <param name="keep_both_reads" type="boolean" label="Always keep both reads (PE specific/palindrome mode)?" truevalue="true" falsevalue="false" checked="true" | |
| 169 help="See help below"/> | |
| 7 | 170 </when> |
| 171 <when value="no" /> <!-- empty clause to satisfy planemo lint --> | |
| 1 | 172 </conditional> |
| 173 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
| 174 <conditional name="operation"> | |
| 7 | 175 <param name="name" type="select" label="Select Trimmomatic operation to perform"> |
| 176 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
| 177 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
| 178 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
| 179 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
| 180 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
| 181 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
| 182 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option> | |
| 183 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option> | |
| 184 </param> | |
| 185 <when value="SLIDINGWINDOW"> | |
| 186 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
| 187 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
| 188 </when> | |
| 189 <when value="MINLEN"> | |
| 190 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
| 191 </when> | |
| 192 <when value="LEADING"> | |
| 193 <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" /> | |
| 194 </when> | |
| 195 <when value="TRAILING"> | |
| 196 <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" /> | |
| 197 </when> | |
| 198 <when value="CROP"> | |
| 199 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
| 200 </when> | |
| 201 <when value="HEADCROP"> | |
| 202 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
| 203 </when> | |
| 204 <when value="AVGQUAL"> | |
| 205 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" /> | |
| 206 </when> | |
| 207 <when value="MAXINFO"> | |
| 208 <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." /> | |
| 209 <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 (<0.2) favours longer reads, high values (>0.8) favours read correctness." /> | |
| 210 </when> | |
| 1 | 211 </conditional> |
| 212 </repeat> | |
| 18 | 213 <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 |
| 214 data, which was sequenced several years ago. FASTQC can be used in order to identify the encoding type."> | |
| 215 <option value="-phred33">Phred33</option> | |
| 216 <option value="-phred64">Phred64</option> | |
| 217 </param> | |
| 12 | 218 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" /> |
| 219 <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)" /> | |
| 1 | 220 </inputs> |
| 221 <outputs> | |
| 7 | 222 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> |
| 223 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> | |
| 1 | 224 </data> |
| 7 | 225 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in"> |
| 226 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> | |
| 1 | 227 </data> |
| 7 | 228 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in"> |
| 229 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> | |
| 1 | 230 </data> |
| 7 | 231 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in"> |
| 232 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> | |
| 1 | 233 </data> |
| 7 | 234 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> |
| 235 <filter>readtype['single_or_paired'] == 'se'</filter> | |
| 1 | 236 </data> |
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237 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired"> |
| 7 | 238 <filter>readtype['single_or_paired'] == "collection"</filter> |
| 239 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> | |
| 240 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> | |
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241 </collection> |
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242 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired"> |
| 7 | 243 <filter>readtype['single_or_paired'] == "collection"</filter> |
| 244 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> | |
| 245 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> | |
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246 </collection> |
| 12 | 247 <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog"> |
| 248 <filter>output_logs</filter> | |
| 249 </data> | |
| 250 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log"> | |
| 251 <filter>output_err</filter> | |
| 252 </data> | |
| 1 | 253 </outputs> |
| 254 <tests> | |
| 255 <test> | |
| 256 <!-- Single-end example --> | |
| 12 | 257 <conditional name="readtype"> |
| 258 <param name="single_or_paired" value="se" /> | |
| 259 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 260 </conditional> | |
| 1 | 261 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> |
| 12 | 262 <param name="output_logs" value="yes" /> |
| 263 <param name="output_err" value="yes" /> | |
| 1 | 264 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> |
| 12 | 265 <output name="log_file" file="trimmomatic_se_out1.log" /> |
| 266 <output name="err_file" file="trimmomatic_se_out1.err" /> | |
| 1 | 267 </test> |
| 268 <test> | |
| 7 | 269 <!-- Single-end example - gzipped --> |
| 270 <param name="single_or_paired" value="se" /> | |
| 271 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> | |
| 272 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 273 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" /> | |
| 274 </test> | |
| 275 <test> | |
| 276 <!-- Paired-end example - gzipped --> | |
| 277 <param name="single_or_paired" value="pair_of_files" /> | |
| 278 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> | |
| 279 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" /> | |
| 280 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 281 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" /> | |
| 282 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" /> | |
| 283 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" /> | |
| 284 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> | |
| 285 </test> | |
| 286 <test> | |
| 1 | 287 <!-- Paired-end example --> |
| 7 | 288 <param name="single_or_paired" value="pair_of_files" /> |
| 1 | 289 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
| 290 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 291 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 292 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
| 293 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 294 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 295 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 296 </test> | |
| 297 <test> | |
| 12 | 298 <!-- Paired-end Illumina 1.3-1.7 quality encoding --> |
| 299 <param name="single_or_paired" value="pair_of_files" /> | |
| 300 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" /> | |
| 301 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" /> | |
| 302 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 303 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" /> | |
| 304 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" /> | |
| 305 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" /> | |
| 306 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" /> | |
| 307 </test> | |
| 308 <test> | |
| 309 <!-- Paired-end Solexa quality encoding --> | |
| 310 <param name="single_or_paired" value="pair_of_files" /> | |
| 311 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" /> | |
| 312 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" /> | |
| 313 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 314 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" /> | |
| 315 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" /> | |
| 316 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" /> | |
| 317 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" /> | |
| 318 </test> | |
| 319 <test> | |
| 1 | 320 <!-- Single-end example (cropping) --> |
| 7 | 321 <param name="single_or_paired" value="se" /> |
| 1 | 322 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
| 323 <param name="operations_0|operation|name" value="CROP" /> | |
| 324 <param name="operations_0|operation|crop" value="10" /> | |
| 325 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> | |
| 326 </test> | |
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327 <test> |
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328 <!-- Paired-end with dataset collection --> |
| 7 | 329 <param name="single_or_paired" value="collection" /> |
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330 <param name="fastq_pair"> |
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331 <collection type="paired"> |
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332 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
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333 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/> |
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334 </collection> |
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335 </param> |
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336 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> |
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337 <output_collection name="fastq_out_paired" type="paired"> |
| 7 | 338 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" /> |
| 339 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
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340 </output_collection> |
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341 <output_collection name="fastq_out_unpaired" type="paired"> |
| 7 | 342 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> |
| 343 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 344 </output_collection> | |
| 345 </test> | |
| 346 <test> | |
| 347 <!-- Paired-end with dataset collection - gzipped --> | |
| 348 <param name="single_or_paired" value="collection" /> | |
| 349 <param name="fastq_pair"> | |
| 350 <collection type="paired"> | |
| 351 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> | |
| 352 <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/> | |
| 353 </collection> | |
| 354 </param> | |
| 355 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 356 <output_collection name="fastq_out_paired" type="paired"> | |
| 357 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" /> | |
| 358 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" /> | |
| 359 </output_collection> | |
| 360 <output_collection name="fastq_out_unpaired" type="paired"> | |
| 361 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" /> | |
| 362 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> | |
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363 </output_collection> |
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364 </test> |
| 4 | 365 <test> |
| 366 <!-- Single-end using AVGQUAL --> | |
| 7 | 367 <param name="single_or_paired" value="se" /> |
| 4 | 368 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
| 369 <param name="operations_0|operation|name" value="AVGQUAL" /> | |
| 370 <param name="operations_0|operation|avgqual" value="30" /> | |
| 371 <output name="fastq_out" file="trimmomatic_avgqual.fastq" /> | |
| 372 </test> | |
| 373 <test> | |
| 374 <!-- Single-end using MAXINFO --> | |
| 7 | 375 <param name="single_or_paired" value="se" /> |
| 4 | 376 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
| 377 <param name="operations_0|operation|name" value="MAXINFO" /> | |
| 378 <param name="operations_0|operation|target_length" value="75" /> | |
| 379 <param name="operations_0|operation|strictness" value="0.8" /> | |
| 380 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" /> | |
| 381 </test> | |
| 9 | 382 <test> |
| 383 <!-- Paired-end ILLUMINACLIP - this does not check valid clipping --> | |
| 384 <param name="single_or_paired" value="pair_of_files" /> | |
| 385 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 386 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 387 <param name="do_illuminaclip" value="true"/> | |
| 388 <param name="adapter_fasta" value="TruSeq2-PE.fa"/> | |
| 389 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 390 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> | |
| 391 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 392 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 393 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> | |
| 394 </test> | |
| 395 <test> | |
| 396 <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping --> | |
| 397 <param name="single_or_paired" value="pair_of_files" /> | |
| 398 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 399 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 400 <param name="do_illuminaclip" value="true"/> | |
| 401 <param name="standard_or_custom" value="custom"/> | |
| 402 <param name="adapter_text" | |
| 403 value=">PrefixPE/1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PrefixPE/2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PCR_Primer1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >PCR_Primer2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer2_rc AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG >FlowCell1 TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC >FlowCell2 TTTTTTTTTTCAAGCAGAAGACGGCATACGA "/> | |
| 404 <param name="adapter_fasta" value="TruSeq2-PE.fa"/> | |
| 405 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 406 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> | |
| 407 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 408 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 409 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> | |
| 410 </test> | |
| 18 | 411 <test> |
| 412 <!-- Quality score test --> | |
| 413 <conditional name="readtype"> | |
| 414 <param name="single_or_paired" value="se" /> | |
| 415 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 416 </conditional> | |
| 417 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 418 <param name="output_logs" value="yes" /> | |
| 419 <param name="output_err" value="yes" /> | |
| 420 <param name="quality_score" value="-phred33"/> | |
| 421 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
| 422 <output name="log_file" file="trimmomatic_se_out1.log" /> | |
| 423 <output name="err_file" file="trimmomatic_se_out2.err" /> | |
| 424 </test> | |
| 1 | 425 </tests> |
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426 <help><![CDATA[ |
| 1 | 427 .. class:: infomark |
| 428 | |
| 429 **What it does** | |
| 430 | |
| 431 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
| 432 single ended data. | |
| 433 | |
| 434 This tool allows the following trimming steps to be performed: | |
| 435 | |
| 436 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
| 9 | 437 |
| 438 * If **Always keep both reads (PE specific/palindrome mode)** is True, the reverse read will also be retained in palindrome mode. | |
| 439 After read-though has been detected by palindrome mode, and the adapter sequence removed, | |
| 440 the reverse read contains the same sequence information as the forward read, albeit in reverse complement. | |
| 441 For this reason, the default behaviour is to entirely drop the reverse read. | |
| 442 Retaining the reverse read may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads. | |
| 1 | 443 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average |
| 444 quality within the window falls below a threshold | |
| 445 * **MINLEN:** Drop the read if it is below a specified length | |
| 446 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
| 447 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
| 448 * **CROP:** Cut the read to a specified length | |
| 449 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
| 4 | 450 * **AVGQUAL:** Drop the read if the average quality is below a specified value |
| 7 | 451 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to |
| 4 | 452 maximise the value of each read |
| 1 | 453 |
| 454 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
| 455 can be mixed and matched and will be performed in the order that they have been | |
| 456 specified. | |
| 457 | |
| 458 .. class:: warningmark | |
| 459 | |
| 460 Note that trimming operation order is important. | |
| 461 | |
| 462 ------------- | |
| 463 | |
| 464 .. class:: infomark | |
| 465 | |
|
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466 **Inputs** |
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467 |
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468 For single-end data this Trimmomatic tool accepts a single FASTQ file; for |
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469 paired-end data it will accept either two FASTQ files (R1 and R2), or a |
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470 dataset collection containing the R1/R2 FASTQ pair. |
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471 |
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472 .. class:: infomark |
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473 |
| 1 | 474 **Outputs** |
| 475 | |
| 476 For paired-end data a particular strength of Trimmomatic is that it retains the | |
| 477 pairing of reads (from R1 and R2) in the filtered output files: | |
| 478 | |
| 479 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
| 480 both have survived filtering. | |
| 481 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
| 482 one of the pair failed the filtering steps. | |
| 483 | |
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484 .. class:: warningmark |
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485 |
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486 If the input consists of a dataset collection with the R1/R2 FASTQ pair then |
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487 the outputs will also inclue two dataset collections: one for the 'paired' |
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488 outputs and one for the 'unpaired' (as described above) |
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489 |
| 1 | 490 Retaining the same order and number of reads in the filtered output fastq files is |
| 491 essential for many downstream analysis tools. | |
| 492 | |
| 493 For single-end data the output is a single FASTQ file containing just the filtered | |
| 494 reads. | |
| 495 | |
| 496 ------------- | |
| 497 | |
| 498 .. class:: infomark | |
| 499 | |
| 500 **Credits** | |
| 501 | |
| 502 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
| 9 | 503 University of Manchester, with contributions from Peter van Heusden, Marius |
| 18 | 504 van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo. |
| 7 | 505 |
| 506 It runs the Trimmomatic program which has been developed | |
| 1 | 507 within Bjorn Usadel's group at RWTH Aachen university. |
| 508 | |
| 509 Trimmomatic website (including documentation): | |
| 510 | |
| 7 | 511 * http://www.usadellab.org/cms/index.php?page=trimmomatic |
| 1 | 512 |
| 513 The reference for Trimmomatic is: | |
| 514 | |
| 515 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer | |
| 516 for Illumina Sequence Data. Bioinformatics, btu170. | |
| 517 | |
| 518 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
| 519 use it. | |
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520 ]]></help> |
| 1 | 521 <citations> |
| 522 <!-- | |
| 523 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 524 Can be either DOI or Bibtex | |
| 525 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 526 --> | |
| 527 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
| 528 </citations> | |
| 529 </tool> |