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comparison trimmomatic.xml @ 15:32f1f56bd970 draft

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Updated for Trimmomatic 0.39 and adds quality score options.
author pjbriggs
date Thu, 02 Mar 2023 15:24:24 +0000
parents d94aff5ee623
children 9a38087e3bfd
comparison
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14:d94aff5ee623 15:32f1f56bd970
1 <tool id="trimmomatic" name="Trimmomatic" version="0.38.1"> 1 <tool id="trimmomatic" name="Trimmomatic" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <macros> 3 <macros>
4 <import>trimmomatic_macros.xml</import> 4 <import>trimmomatic_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.38">trimmomatic</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">trimmomatic</requirement>
8 <!-- 8 <!--
9 Coreutils required for 'readlink -e' work across platforms 9 Coreutils required for 'readlink -e' work across platforms
10 See similar fix for snpSift 10 See similar fix for snpSift
11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
12 --> 12 -->
82 MAXINFO:$op.operation.target_length:$op.operation.strictness 82 MAXINFO:$op.operation.target_length:$op.operation.strictness
83 #end if 83 #end if
84 #end for 84 #end for
85 #if $output_logs: 85 #if $output_logs:
86 -trimlog trimlog 86 -trimlog trimlog
87 #end if
88 #if $quality_score
89 $quality_score
87 #end if 90 #end if
88 2>&1 | tee trimmomatic.log && 91 2>&1 | tee trimmomatic.log &&
89 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi 92 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
90 && 93 &&
91 #if $readtype.single_or_paired == "pair_of_files" 94 #if $readtype.single_or_paired == "pair_of_files"
205 <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." /> 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." />
206 <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 (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." /> 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 (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
207 </when> 210 </when>
208 </conditional> 211 </conditional>
209 </repeat> 212 </repeat>
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>
210 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" /> 218 <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" />
211 <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)" /> 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)" />
212 </inputs> 220 </inputs>
213 <outputs> 221 <outputs>
214 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> 222 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
397 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 405 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
398 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> 406 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
399 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 407 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
400 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> 408 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
401 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> 409 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
410 </test>
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" />
402 </test> 424 </test>
403 </tests> 425 </tests>
404 <help><![CDATA[ 426 <help><![CDATA[
405 .. class:: infomark 427 .. class:: infomark
406 428
477 499
478 **Credits** 500 **Credits**
479 501
480 This Galaxy tool has been developed within the Bioinformatics Core Facility at the 502 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
481 University of Manchester, with contributions from Peter van Heusden, Marius 503 University of Manchester, with contributions from Peter van Heusden, Marius
482 van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt. 504 van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo.
483 505
484 It runs the Trimmomatic program which has been developed 506 It runs the Trimmomatic program which has been developed
485 within Bjorn Usadel's group at RWTH Aachen university. 507 within Bjorn Usadel's group at RWTH Aachen university.
486 508
487 Trimmomatic website (including documentation): 509 Trimmomatic website (including documentation):