# HG changeset patch
# User iuc
# Date 1771576503 0
# Node ID dd0deea7ac0914808621d33aae4125a6d43cbfa4
# Parent  b315ee3d3487af54a635b47b21a7001b7cf2e69c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit 74395802c1621d4b2a169b3953090ad736f6fc70

diff -r b315ee3d3487 -r dd0deea7ac09 hyphy_annotate.xml
--- a/hyphy_annotate.xml	Tue Feb 10 12:13:50 2026 +0000
+++ b/hyphy_annotate.xml	Fri Feb 20 08:35:03 2026 +0000
@@ -9,10 +9,10 @@
         hyphy label-tree
             --tree input.nhx
             --output labeled_tree.nhx
-            #if $regexp:
-                --regexp '$regexp'
+            #if $selection_method.method == 'regexp':
+                --regexp '$selection_method.regexp'
             #else:
-                --list '$list_file'
+                --list '$selection_method.list_file'
             #end if
             --label '$label'
             --reroot '$reroot'
@@ -62,20 +62,50 @@
             <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
             <conditional name="selection_method">
                 <param name="method" value="regexp"/>
-                <param name="regexp" value="USA"/>
+                <param name="regexp" value="_USA_"/>
             </conditional>
             <param name="label" value="Annotated"/>
             <param name="reroot" value="None"/>
             <param name="invert" value="No"/>
             <param name="internal_nodes" value="All descendants"/>
             <param name="leaf_nodes" value="Label"/>
-            <output name="labeled_tree" file="annotate-out1-full.nhx" />
+            <output name="labeled_tree">
+                <assert_contents>
+                    <has_text text="{Annotated}"/>
+                    <has_text text="gb_MW540268"/>
+                    <not_has_text text="REFERENCE{Annotated}"/>
+                    <not_has_text text="gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND{Annotated}"/>
+                </assert_contents>
+            </output>
             <output name="annotate_md_report">
                 <assert_contents>
                     <has_text text="Analysis Description"/>
                 </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="list"/>
+                <param name="list_file" ftype="txt" value="annotate-list1.txt"/>
+            </conditional>
+            <param name="label" value="Annotated"/>
+            <param name="reroot" value="None"/>
+            <param name="invert" value="No"/>
+            <param name="internal_nodes" value="All descendants"/>
+            <param name="leaf_nodes" value="Label"/>
+            <output name="labeled_tree">
+                <assert_contents>
+                    <has_text text="{Annotated}"/>
+                    <has_text text="gb_MW540268"/>
+                    <not_has_text text="REFERENCE{Annotated}"/>
+                </assert_contents>
+            </output>
+            <output name="annotate_md_report">
+                <assert_contents>
+                    <has_text text="Analysis Description"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff -r b315ee3d3487 -r dd0deea7ac09 macros.xml
--- a/macros.xml	Tue Feb 10 12:13:50 2026 +0000
+++ b/macros.xml	Fri Feb 20 08:35:03 2026 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.5.93</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">24.0</token>
     <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>
 
@@ -265,6 +265,7 @@
                 <add value="]"/>
                 <add value="."/>
                 <add value=","/>
+                <add value="_"/>
             </valid>
         </sanitizer>
         <validator type="empty_field" />
diff -r b315ee3d3487 -r dd0deea7ac09 test-data/annotate-list1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotate-list1.txt	Fri Feb 20 08:35:03 2026 +0000
@@ -0,0 +1,5 @@
+gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4
+gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1
+gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1
+epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021
+epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021
diff -r b315ee3d3487 -r dd0deea7ac09 test-data/annotate-out1-full.nhx
--- a/test-data/annotate-out1-full.nhx	Tue Feb 10 12:13:50 2026 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)
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