diff iqtree.xml @ 20:18a61a9c1601 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3

--- a/iqtree.xml	Thu Feb 20 20:11:40 2025 +0000
+++ b/iqtree.xml	Mon May 05 16:50:56 2025 +0000
@@ -715,9 +715,13 @@
         <data name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report">
             <filter>time_tree['date_source']['select_source'] != 'none'</filter>
         </data>
+         <data name="ufboot_out" format="nhx" from_work_dir="*.ufboot" label="${tool.name} on ${on_string}: UFBoot Bootstrap trees">
+            <filter>bootstrap_parameters['ultrafast_bootstrap']['boot_trees'] </filter>
+        </data>
+
     </outputs>
     <tests>
-        <test expect_num_outputs="5">
+        <test expect_num_outputs="6">
             <param name="seed" value="1257" />
             <param name="seqtype" value="DNA" />
             <param name="s" value="example.phy" />
@@ -726,6 +730,7 @@
             <param name="madd" value="LG4M,LG4X" />
             <param name="merit" value="AICc" />
             <param name="ufboot" value="1000" />
+            <param name="boot_trees" value="--boot-trees"/>
             <output name="bionj">
                 <assert_contents>
                     <has_text_matching expression=".*Whale.*" />
@@ -761,6 +766,12 @@
                     <has_line line="END; [Splits]" />
                 </assert_contents>
             </output>
+            <output name="ufboot_out" >
+                <assert_contents>
+                    <has_text text="(LngfishAu" />
+                    <has_text text="(Platypus,Opossum)" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="5">
             <!-- bootstrap sans model -->