Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 4:2801d3cd21ee draft
Updated to Trimmomatic 0.36.
| author | pjbriggs |
|---|---|
| date | Thu, 14 Jul 2016 09:06:00 -0400 |
| parents | a7139c612c45 |
| children | b0315888eb4d |
| rev | line source |
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| 4 | 1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.0"> |
| 1 | 2 <description>flexible read trimming tool for Illumina NGS data</description> |
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3 <requirements> |
| 4 | 4 <requirement type="package" version="0.36">trimmomatic</requirement> |
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5 </requirements> |
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6 <stdio> |
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7 <exit_code range="1:" /> |
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8 </stdio> |
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9 <command interpreter="bash"><![CDATA[ |
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10 trimmomatic.sh |
| 1 | 11 -mx8G |
| 4 | 12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.36.jar |
| 1 | 13 #if $paired_end.is_paired_end |
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14 PE -threads \${GALAXY_SLOTS:-6} -phred33 |
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15 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type |
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16 #if $paired_input_type == "pair_of_files" |
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17 "${paired_end.paired_input_type_conditional.fastq_r1_in}" |
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18 "${paired_end.paired_input_type_conditional.fastq_r2_in}" |
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19 "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}" |
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20 "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}" |
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21 #else |
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22 "${paired_end.paired_input_type_conditional.fastq_pair.forward}" |
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23 "${paired_end.paired_input_type_conditional.fastq_pair.reverse}" |
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24 "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}" |
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25 "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}" |
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26 #end if |
| 1 | 27 #else |
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28 SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out" |
| 1 | 29 #end if |
| 30 ## ILLUMINACLIP option | |
| 31 #if $illuminaclip.do_illuminaclip | |
| 32 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold | |
| 33 #end if | |
| 34 ## Other operations | |
| 35 #for $op in $operations | |
| 36 ## SLIDINGWINDOW | |
| 37 #if str( $op.operation.name ) == "SLIDINGWINDOW" | |
| 38 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality | |
| 39 #end if | |
| 40 ## MINLEN:36 | |
| 41 #if str( $op.operation.name ) == "MINLEN" | |
| 42 MINLEN:$op.operation.minlen | |
| 43 #end if | |
| 44 #if str( $op.operation.name ) == "LEADING" | |
| 45 LEADING:$op.operation.leading | |
| 46 #end if | |
| 47 #if str( $op.operation.name ) == "TRAILING" | |
| 48 TRAILING:$op.operation.trailing | |
| 49 #end if | |
| 50 #if str( $op.operation.name ) == "CROP" | |
| 51 CROP:$op.operation.crop | |
| 52 #end if | |
| 53 #if str( $op.operation.name ) == "HEADCROP" | |
| 54 HEADCROP:$op.operation.headcrop | |
| 55 #end if | |
| 4 | 56 #if str( $op.operation.name ) == "AVGQUAL" |
| 57 AVGQUAL:$op.operation.avgqual | |
| 58 #end if | |
| 59 #if str( $op.operation.name ) == "MAXINFO" | |
| 60 MAXINFO:$op.operation.target_length:$op.operation.strictness | |
| 61 #end if | |
| 1 | 62 #end for |
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63 ]]></command> |
| 1 | 64 <inputs> |
| 65 <conditional name="paired_end"> | |
| 66 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> | |
| 67 <when value="no"> | |
| 68 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> | |
| 69 </when> | |
| 70 <when value="yes"> | |
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71 <conditional name="paired_input_type_conditional"> |
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72 <param name="paired_input_type" type="select" label="Input Type"> |
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73 <option value="pair_of_files" selected="true">Pair of datasets</option> |
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74 <option value="collection">Dataset collection pair</option> |
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75 </param> |
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76 <when value="pair_of_files"> |
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77 <param name="fastq_r1_in" type="data" format="fastqsanger" |
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78 label="Input FASTQ file (R1/first of pair)" /> |
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79 <param name="fastq_r2_in" type="data" format="fastqsanger" |
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80 label="Input FASTQ file (R2/second of pair)" /> |
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81 </when> |
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82 <when value="collection"> |
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83 <param name="fastq_pair" format="fastqsanger" type="data_collection" |
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84 collection_type="paired" |
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85 label="Select FASTQ dataset collection with R1/R2 pair" /> |
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86 </when> |
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87 </conditional> |
| 1 | 88 </when> |
| 89 </conditional> | |
| 90 <conditional name="illuminaclip"> | |
| 91 <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" /> | |
| 92 <when value="yes"> | |
| 93 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
| 94 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
| 95 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
| 96 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
| 97 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
| 98 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
| 99 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
| 100 </param> | |
| 101 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> | |
| 102 <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" /> | |
| 103 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" /> | |
| 104 </when> | |
| 4 | 105 <when value="no" /> <!-- empty clause to satisfy planemo lint --> |
| 1 | 106 </conditional> |
| 107 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
| 108 <conditional name="operation"> | |
| 109 <param name="name" type="select" label="Select Trimmomatic operation to perform"> | |
| 110 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
| 111 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
| 112 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
| 113 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
| 114 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
| 115 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
| 4 | 116 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option> |
| 117 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option> | |
| 1 | 118 </param> |
| 119 <when value="SLIDINGWINDOW"> | |
| 120 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
| 121 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
| 122 </when> | |
| 123 <when value="MINLEN"> | |
| 124 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
| 125 </when> | |
| 126 <when value="LEADING"> | |
| 127 <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" /> | |
| 128 </when> | |
| 129 <when value="TRAILING"> | |
| 130 <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" /> | |
| 131 </when> | |
| 132 <when value="CROP"> | |
| 133 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
| 134 </when> | |
| 135 <when value="HEADCROP"> | |
| 136 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
| 137 </when> | |
| 4 | 138 <when value="AVGQUAL"> |
| 139 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" /> | |
| 140 </when> | |
| 141 <when value="MAXINFO"> | |
| 142 <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." /> | |
| 143 <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." /> | |
| 144 </when> | |
| 1 | 145 </conditional> |
| 146 </repeat> | |
| 147 </inputs> | |
| 148 <outputs> | |
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149 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"> |
| 1 | 150 <filter>paired_end['is_paired_end']</filter> |
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151 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 152 </data> |
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153 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"> |
| 1 | 154 <filter>paired_end['is_paired_end']</filter> |
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155 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 156 </data> |
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157 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"> |
| 1 | 158 <filter>paired_end['is_paired_end']</filter> |
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159 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 160 </data> |
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161 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"> |
| 1 | 162 <filter>paired_end['is_paired_end']</filter> |
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163 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 164 </data> |
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165 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"> |
| 1 | 166 <filter>not paired_end['is_paired_end']</filter> |
| 167 </data> | |
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168 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired"> |
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169 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" /> |
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170 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" /> |
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171 <filter>paired_end['is_paired_end']</filter> |
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172 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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173 </collection> |
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174 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired"> |
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175 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" /> |
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176 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" /> |
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177 <filter>paired_end['is_paired_end']</filter> |
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178 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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179 </collection> |
| 1 | 180 </outputs> |
| 181 <tests> | |
| 182 <test> | |
| 183 <!-- Single-end example --> | |
| 184 <param name="is_paired_end" value="no" /> | |
| 185 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 186 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 187 <!-- | |
| 188 **NB** outputs have to be specified in order that they appear in the | |
| 189 tool (which is the order they will be written to the history) - the | |
| 190 test framework seems to use the order and ignores the "name" attribute | |
| 191 --> | |
| 192 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
| 193 </test> | |
| 194 <test> | |
| 195 <!-- Paired-end example --> | |
| 196 <param name="is_paired_end" value="yes" /> | |
| 197 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 198 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 199 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 200 <!-- | |
| 201 **NB** outputs have to be specified in order that they appear in the | |
| 202 tool (which is the order they will be written to the history) - the | |
| 203 test framework seems to use the order and ignores the "name" attribute | |
| 204 --> | |
| 205 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
| 206 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 207 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 208 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 209 </test> | |
| 210 <test> | |
| 211 <!-- Single-end example (cropping) --> | |
| 212 <param name="is_paired_end" value="no" /> | |
| 213 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 214 <param name="operations_0|operation|name" value="CROP" /> | |
| 215 <param name="operations_0|operation|crop" value="10" /> | |
| 216 <!-- | |
| 217 **NB** outputs have to be specified in order that they appear in the | |
| 218 tool (which is the order they will be written to the history) - the | |
| 219 test framework seems to use the order and ignores the "name" attribute | |
| 220 --> | |
| 221 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> | |
| 222 </test> | |
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223 <test> |
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224 <!-- Paired-end with dataset collection --> |
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225 <param name="is_paired_end" value="yes" /> |
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226 <param name="paired_input_type" value="collection" /> |
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227 <param name="fastq_pair"> |
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228 <collection type="paired"> |
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229 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
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230 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/> |
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231 </collection> |
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232 </param> |
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233 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> |
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234 <output_collection name="fastq_out_paired" type="paired"> |
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235 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" /> |
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236 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" /> |
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237 </output_collection> |
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238 <output_collection name="fastq_out_unpaired" type="paired"> |
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239 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> |
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240 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> |
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241 </output_collection> |
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242 </test> |
| 4 | 243 <test> |
| 244 <!-- Single-end using AVGQUAL --> | |
| 245 <param name="is_paired_end" value="no" /> | |
| 246 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 247 <param name="operations_0|operation|name" value="AVGQUAL" /> | |
| 248 <param name="operations_0|operation|avgqual" value="30" /> | |
| 249 <output name="fastq_out" file="trimmomatic_avgqual.fastq" /> | |
| 250 </test> | |
| 251 <test> | |
| 252 <!-- Single-end using MAXINFO --> | |
| 253 <param name="is_paired_end" value="no" /> | |
| 254 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 255 <param name="operations_0|operation|name" value="MAXINFO" /> | |
| 256 <param name="operations_0|operation|target_length" value="75" /> | |
| 257 <param name="operations_0|operation|strictness" value="0.8" /> | |
| 258 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" /> | |
| 259 </test> | |
| 1 | 260 </tests> |
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261 <help><![CDATA[ |
| 1 | 262 .. class:: infomark |
| 263 | |
| 264 **What it does** | |
| 265 | |
| 266 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
| 267 single ended data. | |
| 268 | |
| 269 This tool allows the following trimming steps to be performed: | |
| 270 | |
| 271 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
| 272 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average | |
| 273 quality within the window falls below a threshold | |
| 274 * **MINLEN:** Drop the read if it is below a specified length | |
| 275 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
| 276 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
| 277 * **CROP:** Cut the read to a specified length | |
| 278 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
| 4 | 279 * **AVGQUAL:** Drop the read if the average quality is below a specified value |
| 280 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to | |
| 281 maximise the value of each read | |
| 1 | 282 |
| 283 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
| 284 can be mixed and matched and will be performed in the order that they have been | |
| 285 specified. | |
| 286 | |
| 287 .. class:: warningmark | |
| 288 | |
| 289 Note that trimming operation order is important. | |
| 290 | |
| 291 ------------- | |
| 292 | |
| 293 .. class:: infomark | |
| 294 | |
|
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295 **Inputs** |
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296 |
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297 For single-end data this Trimmomatic tool accepts a single FASTQ file; for |
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298 paired-end data it will accept either two FASTQ files (R1 and R2), or a |
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299 dataset collection containing the R1/R2 FASTQ pair. |
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300 |
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301 .. class:: infomark |
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302 |
| 1 | 303 **Outputs** |
| 304 | |
| 305 For paired-end data a particular strength of Trimmomatic is that it retains the | |
| 306 pairing of reads (from R1 and R2) in the filtered output files: | |
| 307 | |
| 308 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
| 309 both have survived filtering. | |
| 310 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
| 311 one of the pair failed the filtering steps. | |
| 312 | |
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313 .. class:: warningmark |
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314 |
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315 If the input consists of a dataset collection with the R1/R2 FASTQ pair then |
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316 the outputs will also inclue two dataset collections: one for the 'paired' |
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317 outputs and one for the 'unpaired' (as described above) |
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318 |
| 1 | 319 Retaining the same order and number of reads in the filtered output fastq files is |
| 320 essential for many downstream analysis tools. | |
| 321 | |
| 322 For single-end data the output is a single FASTQ file containing just the filtered | |
| 323 reads. | |
| 324 | |
| 325 ------------- | |
| 326 | |
| 327 .. class:: infomark | |
| 328 | |
| 329 **Credits** | |
| 330 | |
| 331 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
| 332 University of Manchester. It runs the Trimmomatic program which has been developed | |
| 333 within Bjorn Usadel's group at RWTH Aachen university. | |
| 334 | |
| 335 Trimmomatic website (including documentation): | |
| 336 | |
| 337 * http://www.usadellab.org/cms/index.php?page=trimmomatic | |
| 338 | |
| 339 The reference for Trimmomatic is: | |
| 340 | |
| 341 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer | |
| 342 for Illumina Sequence Data. Bioinformatics, btu170. | |
| 343 | |
| 344 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
| 345 use it. | |
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346 ]]></help> |
| 1 | 347 <citations> |
| 348 <!-- | |
| 349 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 350 Can be either DOI or Bibtex | |
| 351 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 352 --> | |
| 353 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
| 354 </citations> | |
| 355 </tool> |