diff hyphy_annotate.xml @ 14:dd0deea7ac09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit 74395802c1621d4b2a169b3953090ad736f6fc70

--- 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[