Mercurial > repos > pjbriggs > trimmomatic
annotate trimmomatic.xml @ 3:a7139c612c45 draft
Updated to version 0.32.3: add support for FASTQ pairs (dataset collections)
| author | pjbriggs |
|---|---|
| date | Wed, 23 Sep 2015 08:48:20 -0400 |
| parents | e7c8359dfa23 |
| children | 2801d3cd21ee |
| rev | line source |
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1 <tool id="trimmomatic" name="Trimmomatic" version="0.32.3"> |
| 1 | 2 <description>flexible read trimming tool for Illumina NGS data</description> |
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3 <requirements> |
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4 <requirement type="package" version="0.32">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 |
| 12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar | |
| 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 | |
| 56 #end for | |
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57 ]]></command> |
| 1 | 58 <inputs> |
| 59 <conditional name="paired_end"> | |
| 60 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> | |
| 61 <when value="no"> | |
| 62 <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" /> | |
| 63 </when> | |
| 64 <when value="yes"> | |
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65 <conditional name="paired_input_type_conditional"> |
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66 <param name="paired_input_type" type="select" label="Input Type"> |
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67 <option value="pair_of_files" selected="true">Pair of datasets</option> |
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68 <option value="collection">Dataset collection pair</option> |
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69 </param> |
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70 <when value="pair_of_files"> |
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71 <param name="fastq_r1_in" type="data" format="fastqsanger" |
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72 label="Input FASTQ file (R1/first of pair)" /> |
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73 <param name="fastq_r2_in" type="data" format="fastqsanger" |
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74 label="Input FASTQ file (R2/second of pair)" /> |
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75 </when> |
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76 <when value="collection"> |
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77 <param name="fastq_pair" format="fastqsanger" type="data_collection" |
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78 collection_type="paired" |
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79 label="Select FASTQ dataset collection with R1/R2 pair" /> |
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80 </when> |
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81 </conditional> |
| 1 | 82 </when> |
| 83 </conditional> | |
| 84 <conditional name="illuminaclip"> | |
| 85 <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" /> | |
| 86 <when value="yes"> | |
| 87 <param name="adapter_fasta" type="select" label="Adapter sequences to use"> | |
| 88 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> | |
| 89 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> | |
| 90 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> | |
| 91 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> | |
| 92 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> | |
| 93 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> | |
| 94 </param> | |
| 95 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> | |
| 96 <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" /> | |
| 97 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" /> | |
| 98 </when> | |
| 99 </conditional> | |
| 100 <repeat name="operations" title="Trimmomatic Operation" min="1"> | |
| 101 <conditional name="operation"> | |
| 102 <param name="name" type="select" label="Select Trimmomatic operation to perform"> | |
| 103 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> | |
| 104 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> | |
| 105 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> | |
| 106 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> | |
| 107 <option value="CROP">Cut the read to a specified length (CROP)</option> | |
| 108 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> | |
| 109 </param> | |
| 110 <when value="SLIDINGWINDOW"> | |
| 111 <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> | |
| 112 <param name="required_quality" type="integer" label="Average quality required" value="20" /> | |
| 113 </when> | |
| 114 <when value="MINLEN"> | |
| 115 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> | |
| 116 </when> | |
| 117 <when value="LEADING"> | |
| 118 <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" /> | |
| 119 </when> | |
| 120 <when value="TRAILING"> | |
| 121 <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" /> | |
| 122 </when> | |
| 123 <when value="CROP"> | |
| 124 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> | |
| 125 </when> | |
| 126 <when value="HEADCROP"> | |
| 127 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> | |
| 128 </when> | |
| 129 </conditional> | |
| 130 </repeat> | |
| 131 </inputs> | |
| 132 <outputs> | |
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133 <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"> |
| 1 | 134 <filter>paired_end['is_paired_end']</filter> |
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135 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 136 </data> |
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137 <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"> |
| 1 | 138 <filter>paired_end['is_paired_end']</filter> |
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139 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 140 </data> |
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141 <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"> |
| 1 | 142 <filter>paired_end['is_paired_end']</filter> |
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143 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 144 </data> |
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145 <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"> |
| 1 | 146 <filter>paired_end['is_paired_end']</filter> |
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147 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> |
| 1 | 148 </data> |
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149 <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"> |
| 1 | 150 <filter>not paired_end['is_paired_end']</filter> |
| 151 </data> | |
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152 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired"> |
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153 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" /> |
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154 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" /> |
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155 <filter>paired_end['is_paired_end']</filter> |
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156 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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157 </collection> |
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158 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired"> |
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159 <data name="forward" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" /> |
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160 <data name="reverse" format="fastqsanger" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" /> |
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161 <filter>paired_end['is_paired_end']</filter> |
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162 <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> |
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163 </collection> |
| 1 | 164 </outputs> |
| 165 <tests> | |
| 166 <test> | |
| 167 <!-- Single-end example --> | |
| 168 <param name="is_paired_end" value="no" /> | |
| 169 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 170 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 171 <!-- | |
| 172 **NB** outputs have to be specified in order that they appear in the | |
| 173 tool (which is the order they will be written to the history) - the | |
| 174 test framework seems to use the order and ignores the "name" attribute | |
| 175 --> | |
| 176 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> | |
| 177 </test> | |
| 178 <test> | |
| 179 <!-- Paired-end example --> | |
| 180 <param name="is_paired_end" value="yes" /> | |
| 181 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 182 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> | |
| 183 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> | |
| 184 <!-- | |
| 185 **NB** outputs have to be specified in order that they appear in the | |
| 186 tool (which is the order they will be written to the history) - the | |
| 187 test framework seems to use the order and ignores the "name" attribute | |
| 188 --> | |
| 189 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> | |
| 190 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> | |
| 191 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> | |
| 192 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> | |
| 193 </test> | |
| 194 <test> | |
| 195 <!-- Single-end example (cropping) --> | |
| 196 <param name="is_paired_end" value="no" /> | |
| 197 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> | |
| 198 <param name="operations_0|operation|name" value="CROP" /> | |
| 199 <param name="operations_0|operation|crop" value="10" /> | |
| 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" file="trimmomatic_se_out2.fastq" /> | |
| 206 </test> | |
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207 <test> |
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208 <!-- Paired-end with dataset collection --> |
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209 <param name="is_paired_end" value="yes" /> |
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210 <param name="paired_input_type" value="collection" /> |
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211 <param name="fastq_pair"> |
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212 <collection type="paired"> |
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213 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> |
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214 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/> |
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215 </collection> |
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216 </param> |
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217 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> |
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218 <output_collection name="fastq_out_paired" type="paired"> |
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219 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" /> |
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220 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" /> |
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221 </output_collection> |
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222 <output_collection name="fastq_out_unpaired" type="paired"> |
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223 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> |
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224 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> |
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225 </output_collection> |
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226 </test> |
| 1 | 227 </tests> |
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228 <help><![CDATA[ |
| 1 | 229 .. class:: infomark |
| 230 | |
| 231 **What it does** | |
| 232 | |
| 233 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and | |
| 234 single ended data. | |
| 235 | |
| 236 This tool allows the following trimming steps to be performed: | |
| 237 | |
| 238 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read | |
| 239 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average | |
| 240 quality within the window falls below a threshold | |
| 241 * **MINLEN:** Drop the read if it is below a specified length | |
| 242 * **LEADING:** Cut bases off the start of a read, if below a threshold quality | |
| 243 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality | |
| 244 * **CROP:** Cut the read to a specified length | |
| 245 * **HEADCROP:** Cut the specified number of bases from the start of the read | |
| 246 | |
| 247 If ILLUMINACLIP is requested then it is always performed first; subsequent options | |
| 248 can be mixed and matched and will be performed in the order that they have been | |
| 249 specified. | |
| 250 | |
| 251 .. class:: warningmark | |
| 252 | |
| 253 Note that trimming operation order is important. | |
| 254 | |
| 255 ------------- | |
| 256 | |
| 257 .. class:: infomark | |
| 258 | |
|
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259 **Inputs** |
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260 |
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261 For single-end data this Trimmomatic tool accepts a single FASTQ file; for |
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262 paired-end data it will accept either two FASTQ files (R1 and R2), or a |
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263 dataset collection containing the R1/R2 FASTQ pair. |
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264 |
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265 .. class:: infomark |
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266 |
| 1 | 267 **Outputs** |
| 268 | |
| 269 For paired-end data a particular strength of Trimmomatic is that it retains the | |
| 270 pairing of reads (from R1 and R2) in the filtered output files: | |
| 271 | |
| 272 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where | |
| 273 both have survived filtering. | |
| 274 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where | |
| 275 one of the pair failed the filtering steps. | |
| 276 | |
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277 .. class:: warningmark |
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278 |
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279 If the input consists of a dataset collection with the R1/R2 FASTQ pair then |
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280 the outputs will also inclue two dataset collections: one for the 'paired' |
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281 outputs and one for the 'unpaired' (as described above) |
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282 |
| 1 | 283 Retaining the same order and number of reads in the filtered output fastq files is |
| 284 essential for many downstream analysis tools. | |
| 285 | |
| 286 For single-end data the output is a single FASTQ file containing just the filtered | |
| 287 reads. | |
| 288 | |
| 289 ------------- | |
| 290 | |
| 291 .. class:: infomark | |
| 292 | |
| 293 **Credits** | |
| 294 | |
| 295 This Galaxy tool has been developed within the Bioinformatics Core Facility at the | |
| 296 University of Manchester. It runs the Trimmomatic program which has been developed | |
| 297 within Bjorn Usadel's group at RWTH Aachen university. | |
| 298 | |
| 299 Trimmomatic website (including documentation): | |
| 300 | |
| 301 * http://www.usadellab.org/cms/index.php?page=trimmomatic | |
| 302 | |
| 303 The reference for Trimmomatic is: | |
| 304 | |
| 305 * Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer | |
| 306 for Illumina Sequence Data. Bioinformatics, btu170. | |
| 307 | |
| 308 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you | |
| 309 use it. | |
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310 ]]></help> |
| 1 | 311 <citations> |
| 312 <!-- | |
| 313 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 314 Can be either DOI or Bibtex | |
| 315 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 316 --> | |
| 317 <citation type="doi">10.1093/bioinformatics/btu170</citation> | |
| 318 </citations> | |
| 319 </tool> |