| Previous changeset 14:d94aff5ee623 (2020-03-26) Next changeset 16:9a38087e3bfd (2024-01-14) |
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Commit message:
Updated for Trimmomatic 0.39 and adds quality score options. |
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modified:
README.rst test-data/trimmomatic_pe_r1_paired_out1.fastq.gz test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz test-data/trimmomatic_pe_r2_paired_out1.fastq.gz test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz test-data/trimmomatic_se_out1.fastq.gz trimmomatic.xml trimmomatic_macros.xml |
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added:
test-data/trimmomatic_se_out2.err |
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| diff -r d94aff5ee623 -r 32f1f56bd970 README.rst --- a/README.rst Thu Mar 26 04:52:47 2020 -0400 +++ b/README.rst Thu Mar 02 15:24:24 2023 +0000 |
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| @@ -71,6 +71,7 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.39 - Update to Trimmomatic 0.39. 0.38.1 - Bug fix: add dependency on ``coreutils`` so that ``readlink -e`` is supported across both Linux and MacOS platforms. 0.38.0 - Update to Trimmomatic 0.38. @@ -121,6 +122,7 @@ Matthias Bernt (@bernt-matthias) added log and trimlog output. Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform support across Linux and MacOS. +Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39. Developers ========== |
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| diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_se_out1.fastq.gz |
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| diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_se_out2.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_se_out2.err Thu Mar 02 15:24:24 2023 +0000 |
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| @@ -0,0 +1,4 @@ +TrimmomaticSE: Started with arguments: + -threads 1 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 -trimlog trimlog -phred33 +Input Reads: 10 Surviving: 8 (80.00%) Dropped: 2 (20.00%) +TrimmomaticSE: Completed successfully |
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| diff -r d94aff5ee623 -r 32f1f56bd970 trimmomatic.xml --- a/trimmomatic.xml Thu Mar 26 04:52:47 2020 -0400 +++ b/trimmomatic.xml Thu Mar 02 15:24:24 2023 +0000 |
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| @@ -1,10 +1,10 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.38.1"> +<tool id="trimmomatic" name="Trimmomatic" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>flexible read trimming tool for Illumina NGS data</description> <macros> <import>trimmomatic_macros.xml</import> </macros> <requirements> - <requirement type="package" version="0.38">trimmomatic</requirement> + <requirement type="package" version="@TOOL_VERSION@">trimmomatic</requirement> <!-- Coreutils required for 'readlink -e' work across platforms See similar fix for snpSift @@ -85,6 +85,9 @@ #if $output_logs: -trimlog trimlog #end if + #if $quality_score + $quality_score + #end if 2>&1 | tee trimmomatic.log && if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && @@ -207,6 +210,11 @@ </when> </conditional> </repeat> + <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 + data, which was sequenced several years ago. FASTQC can be used in order to identify the encoding type."> + <option value="-phred33">Phred33</option> + <option value="-phred64">Phred64</option> + </param> <param name="output_logs" argument="-trimlog" type="boolean" label="Output trimlog file?" truevalue="yes" falsevalue="no" checked="False" /> <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)" /> </inputs> @@ -400,6 +408,20 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> </test> + <test> + <!-- Quality score test --> + <conditional name="readtype"> + <param name="single_or_paired" value="se" /> + <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> + </conditional> + <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> + <param name="output_logs" value="yes" /> + <param name="output_err" value="yes" /> + <param name="quality_score" value="-phred33"/> + <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> + <output name="log_file" file="trimmomatic_se_out1.log" /> + <output name="err_file" file="trimmomatic_se_out2.err" /> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -479,7 +501,7 @@ This Galaxy tool has been developed within the Bioinformatics Core Facility at the University of Manchester, with contributions from Peter van Heusden, Marius -van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt. +van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo. It runs the Trimmomatic program which has been developed within Bjorn Usadel's group at RWTH Aachen university. |
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| diff -r d94aff5ee623 -r 32f1f56bd970 trimmomatic_macros.xml --- a/trimmomatic_macros.xml Thu Mar 26 04:52:47 2020 -0400 +++ b/trimmomatic_macros.xml Thu Mar 02 15:24:24 2023 +0000 |
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| @@ -5,4 +5,6 @@ --> <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token> + <token name="@TOOL_VERSION@">0.39</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> |