Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 5:f80107cdc406 draft
Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
| author | pjbriggs |
|---|---|
| date | Fri, 16 Dec 2016 11:31:55 -0500 |
| parents | 14d05f2d511d |
| children | 141bba0e9a77 |
| rev | line source |
|---|---|
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5
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1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.1"> |
| 0 | 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> |
| 4 | 7 <requirement type="package" version="0.36">trimmomatic</requirement> |
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8 </requirements> |
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9 <stdio> |
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10 <exit_code range="1:" /> |
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11 </stdio> |
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12 <command><![CDATA[ |
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13 @CONDA_TRIMMOMATIC_JAR_PATH@ && |
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14 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ && |
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15 java -mx8G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar |
| 0 | 16 #if $paired_end.is_paired_end |
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17 PE -threads \${GALAXY_SLOTS:-6} -phred33 |
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18 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type |
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19 #if $paired_input_type == "pair_of_files" |
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20 "${paired_end.paired_input_type_conditional.fastq_r1_in}" |
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21 "${paired_end.paired_input_type_conditional.fastq_r2_in}" |
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22 "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}" |
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23 "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}" |
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24 #else |
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25 "${paired_end.paired_input_type_conditional.fastq_pair.forward}" |
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26 "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" |
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27 "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}" |
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28 "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}" |
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29 #end if |
| 0 | 30 #else |
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31 SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out" |
| 0 | 32 #end if |
| 33 ## ILLUMINACLIP option | |
| 34 #if $illuminaclip.do_illuminaclip | |
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35 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold |
| 0 | 36 #end if |
| 37 ## Other operations | |
| 38 #for $op in $operations | |
| 39 ## SLIDINGWINDOW | |
| 40 #if str( $op.operation.name ) == "SLIDINGWINDOW" | |
| 41 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality | |
| 42 #end if | |
| 43 ## MINLEN:36 | |
| 44 #if str( $op.operation.name ) == "MINLEN" | |
| 45 MINLEN:$op.operation.minlen | |
| 46 #end if | |
| 47 #if str( $op.operation.name ) == "LEADING" | |
| 48 LEADING:$op.operation.leading | |
| 49 #end if | |
| 50 #if str( $op.operation.name ) == "TRAILING" | |
| 51 TRAILING:$op.operation.trailing | |
| 52 #end if | |
| 53 #if str( $op.operation.name ) == "CROP" | |
| 54 CROP:$op.operation.crop | |
| 55 #end if | |
| 56 #if str( $op.operation.name ) == "HEADCROP" | |
| 57 HEADCROP:$op.operation.headcrop | |
| 58 #end if | |
| 4 | 59 #if str( $op.operation.name ) == "AVGQUAL" |
| 60 AVGQUAL:$op.operation.avgqual | |
| 61 #end if | |
| 62 #if str( $op.operation.name ) == "MAXINFO" | |
| 63 MAXINFO:$op.operation.target_length:$op.operation.strictness | |
| 64 #end if | |
| 0 | 65 #end for |
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66 2>&1 | tee trimmomatic.log && |
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67 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi |
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68 ]]></command> |
| 0 | 69 <inputs> |
| 70 <conditional name="paired_end"> | |
| 71 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> | |
| 72 <when value="no"> | |
| 73 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> | |
| 74 </when> | |
| 75 <when value="yes"> | |
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76 <conditional name="paired_input_type_conditional"> |
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77 <param name="paired_input_type" type="select" label="Input Type"> |
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78 <option value="pair_of_files" selected="true">Pair of datasets</option> |
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79 <option value="collection">Dataset collection pair</option> |
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80 </param> |
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81 <when value="pair_of_files"> |
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82 <param name="fastq_r1_in" type="data" format="fastqsanger" |
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83 label="Input FASTQ file (R1/first of pair)" /> |
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84 <param name="fastq_r2_in" type="data" format="fastqsanger" |
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85 label="Input FASTQ file (R2/second of pair)" /> |
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86 </when> |
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87 <when value="collection"> |
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88 <param name="fastq_pair" format="fastqsanger" type="data_collection" |
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89 collection_type="paired" |
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90 label="Select FASTQ dataset collection with R1/R2 pair" /> |
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91 </when> |
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92 </conditional> |
| 0 | 93 </when> |
| 94 </conditional> | |
| 95 <conditional name="illuminaclip"> | |
| 96 <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" /> | |
| 97 <when value="yes"> | |
| 98 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
| 99 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
| 100 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
| 101 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
| 102 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
| 103 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
| 104 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
| 105 </param> | |
| 106 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> | |
| 107 <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" /> | |
| 108 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" /> | |
| 109 </when> | |
| 4 | 110 <when value="no" /> <!-- empty clause to satisfy planemo lint --> |
| 0 | 111 </conditional> |
| 112 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
| 113 <conditional name="operation"> | |
| 114 <param name="name" type="select" label="Select Trimmomatic operation to perform"> | |
| 115 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
| 116 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
| 117 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
| 118 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
| 119 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
| 120 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
| 4 | 121 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option> |
| 122 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option> | |
| 0 | 123 </param> |
| 124 <when value="SLIDINGWINDOW"> | |
| 125 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
| 126 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
| 127 </when> | |
| 128 <when value="MINLEN"> | |
| 129 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
| 130 </when> | |
| 131 <when value="LEADING"> | |
| 132 <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" /> | |
| 133 </when> | |
| 134 <when value="TRAILING"> | |
| 135 <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" /> | |
| 136 </when> | |
| 137 <when value="CROP"> | |
| 138 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
| 139 </when> | |
| 140 <when value="HEADCROP"> | |
| 141 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
| 142 </when> | |
| 4 | 143 <when value="AVGQUAL"> |
| 144 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" /> | |
| 145 </when> | |
| 146 <when value="MAXINFO"> | |
| 147 <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." /> | |
| 148 <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." /> | |
| 149 </when> | |
| 0 | 150 </conditional> |
| 151 </repeat> | |
| 152 </inputs> | |
| 153 <outputs> | |
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154 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"> |
| 0 | 155 <filter>paired_end['is_paired_end']</filter> |
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156 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 0 | 157 </data> |
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158 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"> |
| 0 | 159 <filter>paired_end['is_paired_end']</filter> |
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160 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 0 | 161 </data> |
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162 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"> |
| 0 | 163 <filter>paired_end['is_paired_end']</filter> |
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164 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 0 | 165 </data> |
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166 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"> |
| 0 | 167 <filter>paired_end['is_paired_end']</filter> |
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168 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 0 | 169 </data> |
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170 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"> |
| 0 | 171 <filter>not paired_end['is_paired_end']</filter> |
| 172 </data> | |
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173 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired"> |
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174 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" /> |
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175 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" /> |
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176 <filter>paired_end['is_paired_end']</filter> |
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177 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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178 </collection> |
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179 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired"> |
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180 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" /> |
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181 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" /> |
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182 <filter>paired_end['is_paired_end']</filter> |
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183 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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184 </collection> |
| 0 | 185 </outputs> |
| 186 <tests> | |
| 187 <test> | |
| 188 <!-- Single-end example --> | |
| 189 <param name="is_paired_end" value="no" /> | |
| 190 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 191 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 192 <!-- | |
| 193 **NB** outputs have to be specified in order that they appear in the | |
| 194 tool (which is the order they will be written to the history) - the | |
| 195 test framework seems to use the order and ignores the "name" attribute | |
| 196 --> | |
| 197 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
| 198 </test> | |
| 199 <test> | |
| 200 <!-- Paired-end example --> | |
| 201 <param name="is_paired_end" value="yes" /> | |
| 202 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 203 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 204 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 205 <!-- | |
| 206 **NB** outputs have to be specified in order that they appear in the | |
| 207 tool (which is the order they will be written to the history) - the | |
| 208 test framework seems to use the order and ignores the "name" attribute | |
| 209 --> | |
| 210 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
| 211 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 212 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 213 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 214 </test> | |
| 215 <test> | |
| 216 <!-- Single-end example (cropping) --> | |
| 217 <param name="is_paired_end" value="no" /> | |
| 218 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 219 <param name="operations_0|operation|name" value="CROP" /> | |
| 220 <param name="operations_0|operation|crop" value="10" /> | |
| 221 <!-- | |
| 222 **NB** outputs have to be specified in order that they appear in the | |
| 223 tool (which is the order they will be written to the history) - the | |
| 224 test framework seems to use the order and ignores the "name" attribute | |
| 225 --> | |
| 226 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> | |
| 227 </test> | |
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228 <test> |
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229 <!-- Paired-end with dataset collection --> |
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230 <param name="is_paired_end" value="yes" /> |
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231 <param name="paired_input_type" value="collection" /> |
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232 <param name="fastq_pair"> |
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233 <collection type="paired"> |
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234 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
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235 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/> |
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236 </collection> |
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237 </param> |
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238 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> |
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239 <output_collection name="fastq_out_paired" type="paired"> |
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240 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" /> |
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241 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" /> |
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242 </output_collection> |
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243 <output_collection name="fastq_out_unpaired" type="paired"> |
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244 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> |
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245 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> |
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246 </output_collection> |
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247 </test> |
| 4 | 248 <test> |
| 249 <!-- Single-end using AVGQUAL --> | |
| 250 <param name="is_paired_end" value="no" /> | |
| 251 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 252 <param name="operations_0|operation|name" value="AVGQUAL" /> | |
| 253 <param name="operations_0|operation|avgqual" value="30" /> | |
| 254 <output name="fastq_out" file="trimmomatic_avgqual.fastq" /> | |
| 255 </test> | |
| 256 <test> | |
| 257 <!-- Single-end using MAXINFO --> | |
| 258 <param name="is_paired_end" value="no" /> | |
| 259 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 260 <param name="operations_0|operation|name" value="MAXINFO" /> | |
| 261 <param name="operations_0|operation|target_length" value="75" /> | |
| 262 <param name="operations_0|operation|strictness" value="0.8" /> | |
| 263 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" /> | |
| 264 </test> | |
| 0 | 265 </tests> |
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266 <help><![CDATA[ |
| 0 | 267 .. class:: infomark |
| 268 | |
| 269 **What it does** | |
| 270 | |
| 271 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
| 272 single ended data. | |
| 273 | |
| 274 This tool allows the following trimming steps to be performed: | |
| 275 | |
| 276 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
| 277 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average | |
| 278 quality within the window falls below a threshold | |
| 279 * **MINLEN:** Drop the read if it is below a specified length | |
| 280 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
| 281 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
| 282 * **CROP:** Cut the read to a specified length | |
| 283 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
| 4 | 284 * **AVGQUAL:** Drop the read if the average quality is below a specified value |
| 285 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to | |
| 286 maximise the value of each read | |
| 0 | 287 |
| 288 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
| 289 can be mixed and matched and will be performed in the order that they have been | |
| 290 specified. | |
| 291 | |
| 292 .. class:: warningmark | |
| 293 | |
| 294 Note that trimming operation order is important. | |
| 295 | |
| 296 ------------- | |
| 297 | |
| 298 .. class:: infomark | |
| 299 | |
|
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300 **Inputs** |
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301 |
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302 For single-end data this Trimmomatic tool accepts a single FASTQ file; for |
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303 paired-end data it will accept either two FASTQ files (R1 and R2), or a |
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304 dataset collection containing the R1/R2 FASTQ pair. |
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305 |
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306 .. class:: infomark |
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307 |
| 0 | 308 **Outputs** |
| 309 | |
| 310 For paired-end data a particular strength of Trimmomatic is that it retains the | |
| 311 pairing of reads (from R1 and R2) in the filtered output files: | |
| 312 | |
| 313 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
| 314 both have survived filtering. | |
| 315 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
| 316 one of the pair failed the filtering steps. | |
| 317 | |
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318 .. class:: warningmark |
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319 |
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320 If the input consists of a dataset collection with the R1/R2 FASTQ pair then |
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321 the outputs will also inclue two dataset collections: one for the 'paired' |
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322 outputs and one for the 'unpaired' (as described above) |
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323 |
| 0 | 324 Retaining the same order and number of reads in the filtered output fastq files is |
| 325 essential for many downstream analysis tools. | |
| 326 | |
| 327 For single-end data the output is a single FASTQ file containing just the filtered | |
| 328 reads. | |
| 329 | |
| 330 ------------- | |
| 331 | |
| 332 .. class:: infomark | |
| 333 | |
| 334 **Credits** | |
| 335 | |
| 336 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
| 337 University of Manchester. It runs the Trimmomatic program which has been developed | |
| 338 within Bjorn Usadel's group at RWTH Aachen university. | |
| 339 | |
| 340 Trimmomatic website (including documentation): | |
| 341 | |
| 342 * http://www.usadellab.org/cms/index.php?page=trimmomatic | |
| 343 | |
| 344 The reference for Trimmomatic is: | |
| 345 | |
| 1 | 346 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer |
| 347 for Illumina Sequence Data. Bioinformatics, btu170. | |
| 0 | 348 |
| 349 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
| 350 use it. | |
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351 ]]></help> |
| 1 | 352 <citations> |
| 353 <!-- | |
| 354 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 355 Can be either DOI or Bibtex | |
| 356 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 357 --> | |
| 358 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
| 359 </citations> | |
| 0 | 360 </tool> |