# HG changeset patch
# User iuc
# Date 1739448407 0
# Node ID 4f4e34a75de9e9e476505b7e0bbd31e2a67b6f39
# Parent  c456a40153afd49305f8286672e3e2f873ae2936
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab

diff -r c456a40153af -r 4f4e34a75de9 bbduk.xml
--- a/bbduk.xml	Tue Nov 19 14:46:33 2024 +0000
+++ b/bbduk.xml	Thu Feb 13 12:06:47 2025 +0000
@@ -142,6 +142,9 @@
         enthist='${output_enthist}'
     #end if
 #end if
+#if $log_file
+    2> >(tee '$log_output' >&2)
+#end if
 t=\${GALAXY_SLOTS:-4}
 ]]></command>
     <inputs>
@@ -226,6 +229,7 @@
                 </param>
             </when>
         </conditional>
+        <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
     </inputs>
     <outputs>
         <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
@@ -283,15 +287,32 @@
         <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
             <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
         </data>
+        <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)">
+            <filter>log_file</filter>
+        </data>
     </outputs>
     <tests>
         <!-- Single read -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
             <param name="reference_type" value="files"/>
             <param name="outputs_select" value="outu"/>
+            <param name="log_file" value="true"/>
             <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
+            <output name="log_output" ftype="txt">
+                <assert_contents>
+                    <has_text text="Executing jgi.BBDuk"/>
+                    <has_text text="Input"/>
+                    <has_text text="Contaminants"/>
+                    <has_text text="Total Removed"/>
+                    <has_text text="Result"/>
+                    <has_text text="10000 bases"/>
+                    <has_text text="100 reads"/>
+                    <has_text text="0 reads"/>
+                    <has_text text="0 bases"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- Paired reads in separate datasets -->
         <test expect_num_outputs="4">
@@ -349,4 +370,4 @@
  * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>
\ No newline at end of file
diff -r c456a40153af -r 4f4e34a75de9 macros.xml
--- a/macros.xml	Tue Nov 19 14:46:33 2024 +0000
+++ b/macros.xml	Thu Feb 13 12:06:47 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">39.08</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>