# HG changeset patch
# User pjbriggs
# Date 1677770664 0
# Node ID 32f1f56bd970a9b518d5a65e6541d5b2a2d67b43
# Parent  d94aff5ee62311268e0b74dc90385108078fed10
Updated for Trimmomatic 0.39 and adds quality score options.

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
@@ -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
 ==========
diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_pe_r1_paired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r1_paired_out1.fastq.gz has changed
diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz has changed
diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_pe_r2_paired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r2_paired_out1.fastq.gz has changed
diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz has changed
diff -r d94aff5ee623 -r 32f1f56bd970 test-data/trimmomatic_se_out1.fastq.gz
Binary file test-data/trimmomatic_se_out1.fastq.gz has changed
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
@@ -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
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
@@ -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.
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
@@ -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>