# HG changeset patch
# User iuc
# Date 1739475375 0
# Node ID ab208c87d9730176d581f2eccf4a567c355e7382
# Parent  a96f3ad4e0d898a5dd61811df64fdaaa9419a038
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit acac4f9e3f82cc7248177b97d1cbabbf58d24cf6

diff -r a96f3ad4e0d8 -r ab208c87d973 megahit_wrapper.xml
--- a/megahit_wrapper.xml	Tue Nov 28 07:47:49 2023 +0000
+++ b/megahit_wrapper.xml	Thu Feb 13 19:36:15 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy1">
+<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy2">
     <description>for metagenomics assembly</description>
     <macros>
         <token name="@TOOL_VERSION@">1.2.9</token>
@@ -56,7 +56,6 @@
     ${advanced_section.kmin1pass}
     --min-contig-len '${output_section.min_contig_len}'
     \$MEMORY
-&& cat megahit_out/log
     ]]></command>
     <inputs>
         <conditional name="input_option">
@@ -123,6 +122,7 @@
         <section name="output_section" title="Output options" expanded="True">
             <param argument="--min-contig-len" type="integer" value="200" label="Minimum length of contigs to output" />
             <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
+            <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
         </section>
     </inputs>
     <outputs>
@@ -131,18 +131,30 @@
             <filter>output_section['show_intermediate_contigs']</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.*\d)\.contigs\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" />
         </collection>
+        <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)" from_work_dir="megahit_out/log">
+            <filter>output_section['log_file']</filter>
+        </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <conditional name="input_option">
                 <param name="choice" value="single"/>
                 <param name="single_files" value="refExample.fa" ftype="fasta"/>
             </conditional>
+            <param name="log_file" value="true"/>
             <output name="output">
             <assert_contents>
-              <has_line_matching expression=">k21_0 flag=3 multi=1.0486 len=576" />
+              <has_line_matching expression=">k21_0 flag=3 multi=1.0505 len=576" />
             </assert_contents>
             </output>
+            <output name="log_output">
+                <assert_contents>
+                    <has_text text="- MEGAHIT v"/>
+                    <has_text text="- Build graph for k = 21"/>
+                    <has_text text="- Assemble contigs from SdBG for k = 21"/>
+                    <has_text text="- Local assembly for k = 21"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
              <conditional name="input_option">