--- a/trimmomatic.xml	Mon Mar 05 05:33:13 2018 -0500
+++ b/trimmomatic.xml	Fri Oct 05 03:30:28 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.36.5">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.6">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>
@@ -24,12 +24,12 @@
   #end if
   java \${_JAVA_OPTIONS:--Xmx8G} -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
   #if $readtype.single_or_paired in ["pair_of_files","collection"]
-    PE -threads \${GALAXY_SLOTS:-6} -phred33
+    PE -threads \${GALAXY_SLOTS:-6}
       fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
       fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
       fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
   #else
-    SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
+    SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
   #end if
   ## ILLUMINACLIP option
   #if $illuminaclip.do_illuminaclip
@@ -76,6 +76,9 @@
       MAXINFO:$op.operation.target_length:$op.operation.strictness
     #end if
   #end for
+  #if $output_logs:
+    -trimlog trimlog
+  #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
   &&
@@ -109,16 +112,16 @@
          <option value="collection">Paired-end (as collection)</option>
       </param>
     <when value="se">
-      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
+      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
     </when>
     <when value="pair_of_files">
-      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
+      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R1/first of pair)" />
-      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz"
+      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
          label="Input FASTQ file (R2/second of pair)" />
     </when>
       <when value="collection">
-        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
+        <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
       </when>
     </conditional>
     <conditional name="illuminaclip">
@@ -198,6 +201,8 @@
         </when>
       </conditional>
     </repeat>
+    <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>
   <outputs>
     <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
@@ -225,15 +230,26 @@
         <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
         <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
     </collection>
-
+    <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
+      <filter>output_logs</filter>
+    </data>
+    <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">
+      <filter>output_err</filter>
+    </data>
   </outputs>
   <tests>
     <test>
       <!-- Single-end example -->
-      <param name="single_or_paired" value="se" />
-      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      <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" />
       <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" />
     </test>
     <test>
       <!-- Single-end example - gzipped -->
@@ -265,6 +281,28 @@
       <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
     </test>
     <test>
+      <!-- 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" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" />
+      <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>
+      <!-- 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" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" />
+      <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>
       <!-- Single-end example (cropping) -->
       <param name="single_or_paired" value="se" />
       <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
@@ -435,7 +473,7 @@
 
 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 and Charles Girardot.
+van den Beek, Jelle Scholtalbers, Charles Girardot, and Matthias Bernt.
 
 It runs the Trimmomatic program which has been developed
 within Bjorn Usadel's group at RWTH Aachen university.