# HG changeset patch
# User iuc
# Date 1740173421 0
# Node ID eca2e2e204360bcc2128a9068913c7a1bec66f91
# Parent  740fd2d16a28741174f9dcc6ada10aacc181c8fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit e567b31e44ef8525e6667b37480b6f1b599224b9

diff -r 740fd2d16a28 -r eca2e2e20436 metaphlan.xml
--- a/metaphlan.xml	Fri Sep 20 20:14:38 2024 +0000
+++ b/metaphlan.xml	Fri Feb 21 21:30:21 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
+<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
     <description>to profile the composition of microbial communities</description>
     <macros>
         <import>macros.xml</import>
@@ -183,6 +183,7 @@
 #if 'ignore_archaea' in $analysis.organism_profiling
     --ignore_archaea
 #end if
+    --stat $analysis.stat
     --stat_q $analysis.stat_q
     --perc_nonzero $analysis.perc_nonzero
 #if $analysis.ignore_markers
@@ -1139,14 +1140,6 @@
                     <param name="cached_db" value="test-db-20210409"/>
                 </conditional>
             </section>
-            <conditional name="in">
-                <param name="selector" value="bowtie2out"/>
-                <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
-            </conditional>
-            <section name="mapping">
-                <param name="bt2_ps" value="sensite"/>
-                <param name="min_mapq_val" value="5"/>
-            </section>
             <section name="analysis">
                 <conditional name="analysis_type">
                     <param name="t" value="rel_ab"/>
@@ -1354,7 +1347,6 @@
             </section>
             <conditional name="viral_analysis">
                 <param name="profile_vsc" value="--profile_vsc"/>
-                <param name="vsc_out" value="true"/>
             </conditional>
             <conditional name="subsample">
                 <param name="selector" value="single"/>