Mercurial > repos > pjbriggs > trimmomatic
comparison trimmomatic.xml @ 15:32f1f56bd970 draft
Updated for Trimmomatic 0.39 and adds quality score options.
author | pjbriggs |
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date | Thu, 02 Mar 2023 15:24:24 +0000 |
parents | d94aff5ee623 |
children | 9a38087e3bfd |
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14:d94aff5ee623 | 15:32f1f56bd970 |
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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 (<0.2) favours longer reads, high values (>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 (<0.2) favours longer reads, high values (>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): |