--- a/scoary.xml	Sun Mar 21 12:21:41 2021 +0000
+++ b/scoary.xml	Mon Mar 11 21:49:00 2024 +0000
@@ -3,6 +3,9 @@
     <macros>
         <token name="@TOOL_VERSION@">1.6.16</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">scoary</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>
     </requirements>
@@ -75,7 +78,7 @@
             </repeat>
             <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />
             <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />
-            <param name="collapse" argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
+            <param argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
             <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." />
         </section>