# HG changeset patch
# User iuc
# Date 1751288117 0
# Node ID 295b25fe8e251693e103221b808869ec0cd25280
# Parent  77d50ec2bcf269d2595ce4febe49f310657a02d2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit e84f1b29e95e7fbf7d8fdd7df366073555f1a012

diff -r 77d50ec2bcf2 -r 295b25fe8e25 scoary.xml
--- a/scoary.xml	Mon Mar 11 21:49:00 2024 +0000
+++ b/scoary.xml	Mon Jun 30 12:55:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">
+<tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy1" profile="24.2">
     <description>calculates the assocations between all genes in the accessory genome and the traits</description>
     <macros>
         <token name="@TOOL_VERSION@">1.6.16</token>
@@ -54,8 +54,11 @@
 
 --no-time
 &&
-tail -n +1 *.csv | sed "s/\,/\\t/g" > scoary_output.tsv &&
-mv *.nwk scoary_output.nwk
+tail -n +1 *.csv | sed "s/\,/\\t/g" > scoary_output.tsv
+#if $output_options.upgma
+    &&
+    mv *.nwk scoary_output.nwk
+#end if
 
     ]]></command>
     <inputs>
@@ -94,14 +97,18 @@
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="input_traits" ftype="csv" value="Tetracycline_resistance.csv" />
             <param name="input_genes" ftype="csv" value="Gene_presence_absence.csv" />
-            <param name="upgma" value="Yes" />
-            <repeat name="series_pc">
-                <param name="pvalue" value="0.05"/>
-                <param name="correction" value="I"/>
-            </repeat>
+            <section name="output_options">
+                <param name="upgma" value="false" />
+            </section>
+            <section name="additional_options">
+                <repeat name="series_pc">
+                    <param name="pvalue" value="0.05"/>
+                    <param name="correction" value="I"/>
+                </repeat>
+            </section>
             <output name="out_tabular" file="scoary_output.tsv" ftype="tabular" sort="true">
                 <assert_contents>
                     <has_n_lines n="573" />
@@ -109,20 +116,23 @@
                     <has_line line="==&gt; Tetracycline_resistance.results.csv &lt;==" />
                 </assert_contents>
             </output>
-            <output name="out_newick" file="scoary_output.nwk" ftype="newick" />
         </test>
         <test expect_num_outputs="2">
             <param name="input_traits" ftype="csv" value="Tetracycline_resistance.csv" />
             <param name="input_genes" ftype="csv" value="Gene_presence_absence.csv" />
-            <param name="upgma" value="Yes" />
-            <repeat name="series_pc">
-                <param name="pvalue" value="0.05"/>
-                <param name="correction" value="I"/>
-            </repeat>
-            <repeat name="series_pc">
-                <param name="pvalue" value="0.05"/>
-                <param name="correction" value="EPW"/>
-            </repeat>
+            <section name="output_options">
+                <param name="upgma" value="true" />
+            </section>
+            <section name="additional_options">
+                <repeat name="series_pc">
+                    <param name="pvalue" value="0.05"/>
+                    <param name="correction" value="I"/>
+                </repeat>
+                <repeat name="series_pc">
+                    <param name="pvalue" value="0.05"/>
+                    <param name="correction" value="EPW"/>
+                </repeat>
+            </section>
             <output name="out_tabular" file="scoary_output_2.tsv" ftype="tabular" sort="true">
                 <assert_contents>
                     <has_n_lines n="27" />