# HG changeset patch
# User iuc
# Date 1710699007 0
# Node ID 746b434c8fbbc2cfd570196f196f71421094fef2
# Parent  8f6c7638eab2ad956997a30ceb4308415f64e979
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 5de7b91f2bda9c351f9512601f899248b7278924

diff -r 8f6c7638eab2 -r 746b434c8fbb macros.xml
--- a/macros.xml	Sun Dec 19 15:53:23 2021 +0000
+++ b/macros.xml	Sun Mar 17 18:10:07 2024 +0000
@@ -1,13 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.1</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
-    <xml name="edam_ontology">
-        <edam_topics>                                                                                  
-            <edam_topic>topic_0194</edam_topic>
-        </edam_topics>
-        <edam_operations>
-            <edam_operation>operation_0540</edam_operation>
-        </edam_operations>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">usher</xref>
+        </xrefs>
     </xml>
     <xml name="requirements">
         <requirements>
diff -r 8f6c7638eab2 -r 746b434c8fbb usher.xml
--- a/usher.xml	Sun Dec 19 15:53:23 2021 +0000
+++ b/usher.xml	Sun Mar 17 18:10:07 2024 +0000
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro='edam_ontology' />
+    <expand macro="xrefs"/>
     <expand macro='requirements' />
     <version_command>usher --version</version_command>
     <command detect_errors='exit_code'><![CDATA[
@@ -42,9 +42,7 @@
         #if $output_options.multiple_placements
             -M $output_options.multiple_placements
         #end if
-        #if $retain_input_branch_lengths
-            $retain_input_branch_lengths
-        #end if
+        $retain_input_branch_lengths
         -T \${GALAXY_SLOTS:-1}
         -d ./
         #if $output_options.write_subtrees_size
@@ -299,7 +297,7 @@
         <test expect_num_outputs="3">
             <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
             <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb" ftype="protobuf3"/>
-            <param name="retain_input_branch" value="true"/>
+            <param name="retain_input_branch_lengths" value="true"/>
             <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
             <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
             <output name="clades" ftype="txt">