# HG changeset patch
# User iuc
# Date 1772052899 0
# Node ID 387915b575e0b7fefc7fe5f6680d9c682909b6c2
# Parent  ad96aea7802a7297ec028067fc891e6a969b4ab3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit 00107ff4b116892cd55d7aa5bfd1ee1855d511af

diff -r ad96aea7802a -r 387915b575e0 hyphy_annotate.xml
--- a/hyphy_annotate.xml	Fri Feb 20 08:30:38 2026 +0000
+++ b/hyphy_annotate.xml	Wed Feb 25 20:54:59 2026 +0000
@@ -16,7 +16,7 @@
             #end if
             --label '$label'
             --reroot '$reroot'
-            '$invert'
+            $invert
             --internal-nodes '$internal_nodes'
             --leaf-nodes '$leaf_nodes'
             > annotate_stdout.md 2>/dev/null
@@ -66,7 +66,7 @@
             </conditional>
             <param name="label" value="Annotated"/>
             <param name="reroot" value="None"/>
-            <param name="invert" value="No"/>
+            <param name="invert" value="false"/>
             <param name="internal_nodes" value="All descendants"/>
             <param name="leaf_nodes" value="Label"/>
             <output name="labeled_tree">
@@ -91,7 +91,7 @@
             </conditional>
             <param name="label" value="Annotated"/>
             <param name="reroot" value="None"/>
-            <param name="invert" value="No"/>
+            <param name="invert" value="false"/>
             <param name="internal_nodes" value="All descendants"/>
             <param name="leaf_nodes" value="Label"/>
             <output name="labeled_tree">
@@ -107,6 +107,31 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="2">
+            <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
+            <conditional name="selection_method">
+                <param name="method" value="regexp"/>
+                <param name="regexp" value="_USA_"/>
+            </conditional>
+            <param name="label" value="Annotated"/>
+            <param name="reroot" value="None"/>
+            <param name="invert" value="true"/>
+            <param name="internal_nodes" value="All descendants"/>
+            <param name="leaf_nodes" value="Label"/>
+            <output name="labeled_tree">
+                <assert_contents>
+                    <has_text text="{Annotated}"/>
+                    <not_has_text text="gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA{Annotated}"/>
+                    <has_text text="REFERENCE{Annotated}"/>
+                    <has_text text="gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND"/>
+                </assert_contents>
+            </output>
+            <output name="annotate_md_report">
+                <assert_contents>
+                    <has_text text="Analysis Description"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 HyPhy Annotate (label-tree)
diff -r ad96aea7802a -r 387915b575e0 macros.xml
--- a/macros.xml	Fri Feb 20 08:30:38 2026 +0000
+++ b/macros.xml	Wed Feb 25 20:54:59 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.5.93</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>