--- a/trimmomatic.xml	Thu Mar 02 15:24:24 2023 +0000
+++ b/trimmomatic.xml	Sun Jan 14 11:00:33 2024 +0000
@@ -10,7 +10,7 @@
 	See similar fix for snpSift
 	https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
     -->
-    <requirement type="package" version="8.25">coreutils</requirement>
+    <requirement type="package" version="9.4">coreutils</requirement>
   </requirements>
   <command detect_errors="aggressive"><![CDATA[
   @CONDA_TRIMMOMATIC_JAR_PATH@ &&
@@ -38,7 +38,7 @@
     SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
   #end if
   ## ILLUMINACLIP option
-  #if $illuminaclip.do_illuminaclip
+  #if $illuminaclip.do_illuminaclip == "yes"
     #if $illuminaclip.adapter_type.standard_or_custom == "custom"
       #if $readtype.single_or_paired in ["pair_of_files","collection"]
         ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
@@ -134,7 +134,10 @@
       </when>
     </conditional>
     <conditional name="illuminaclip">
-      <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="False" />
+      <param name="do_illuminaclip" type="select" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read">
+	<option value="no" selected="true">no</option>
+	<option value="yes">yes</option>
+      </param>
       <when value="yes">
         <conditional name="adapter_type">
           <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?">
@@ -252,7 +255,7 @@
     </data>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="3">
       <!-- Single-end example -->
       <conditional name="readtype">
         <param name="single_or_paired" value="se" />
@@ -263,16 +266,16 @@
       <param name="output_err" value="yes" />
       <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_out1.err" />
+      <output name="err_file" compare="re_match" file="trimmomatic_se_out1.err.re_match" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <!-- Single-end example - gzipped -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
       <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
     </test>
-    <test>
+    <test expect_num_outputs="4">
       <!-- Paired-end example - gzipped -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
@@ -283,7 +286,7 @@
       <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
       <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
     </test>
-    <test>
+    <test expect_num_outputs="4">
       <!-- Paired-end example -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -294,7 +297,7 @@
       <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.fastq" />
     </test>
-    <test>
+    <test expect_num_outputs="4">
       <!-- Paired-end Illumina 1.3-1.7 quality encoding -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" />
@@ -305,7 +308,7 @@
       <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" />
       <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" />
     </test>
-    <test>
+    <test expect_num_outputs="4">
       <!-- Paired-end Solexa quality encoding -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" />
@@ -316,7 +319,7 @@
       <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" />
       <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <!-- Single-end example (cropping) -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -324,7 +327,7 @@
       <param name="operations_0|operation|crop" value="10" />
       <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
     </test>
-    <test>
+    <test expect_num_outputs="6">
       <!-- Paired-end with dataset collection -->
       <param name="single_or_paired" value="collection" />
       <param name="fastq_pair">
@@ -343,7 +346,7 @@
         <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
       </output_collection>
     </test>
-    <test>
+    <test expect_num_outputs="6">
       <!-- Paired-end with dataset collection - gzipped -->
       <param name="single_or_paired" value="collection" />
       <param name="fastq_pair">
@@ -362,7 +365,7 @@
         <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
       </output_collection>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <!-- Single-end using AVGQUAL -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -370,7 +373,7 @@
       <param name="operations_0|operation|avgqual" value="30" />
       <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <!-- Single-end using MAXINFO -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -379,12 +382,12 @@
       <param name="operations_0|operation|strictness" value="0.8" />
       <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
     </test>
-    <test>
+    <test expect_num_outputs="4">
       <!-- Paired-end ILLUMINACLIP - this does not check valid clipping -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
-      <param name="do_illuminaclip" value="true"/>
+      <param name="do_illuminaclip" value="yes"/>
       <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
       <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
       <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
@@ -392,12 +395,12 @@
       <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>
+    <test expect_num_outputs="4">
       <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping -->
       <param name="single_or_paired" value="pair_of_files" />
       <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
       <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
-      <param name="do_illuminaclip" value="true"/>
+      <param name="do_illuminaclip" value="yes"/>
       <param name="standard_or_custom" value="custom"/>
       <param name="adapter_text"
              value=">PrefixPE/1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PrefixPE/2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PCR_Primer1_rc&#10;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT&#10;>PCR_Primer2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer2_rc&#10;AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG&#10;>FlowCell1&#10;TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC&#10;>FlowCell2&#10;TTTTTTTTTTCAAGCAGAAGACGGCATACGA&#10;"/>
@@ -408,7 +411,7 @@
       <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>
+    <test expect_num_outputs="3">
       <!-- Quality score test -->
       <conditional name="readtype">
         <param name="single_or_paired" value="se" />
@@ -420,7 +423,7 @@
       <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" />
+      <output name="err_file" compare="re_match" file="trimmomatic_se_out2.err.re_match" />
     </test>
   </tests>
   <help><![CDATA[
@@ -499,9 +502,11 @@
 
 **Credits**
 
-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, Matthias Bernt and Cristóbal Gallardo.
+This Galaxy tool was originally 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, Matthias
+Bernt and Cristóbal Gallardo. It is now maintained as part of the IUC tool
+collection.
 
 It runs the Trimmomatic program which has been developed
 within Bjorn Usadel's group at RWTH Aachen university.