Replace EDAM by bio.tools in usher (#5869)

* Replace EDAM by bio.tools in usher * replace obsolete edam_ontology macro * Update matutils.xml * fix another linter warning --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyproject · Mar 17, 2024 · 5de7b91 · 5de7b91
1 parent ab75ba7
commit 5de7b91
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Showing 3 changed files with 9 additions and 14 deletions.
diff --git a/tools/usher/macros.xml b/tools/usher/macros.xml
@@ -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 --git a/tools/usher/matutils.xml b/tools/usher/matutils.xml
@@ -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[
@@ -281,7 +281,7 @@
         <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats">
             <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter>
         </data>  
-        <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation annotated tree">
+        <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation tree">
             <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter>
         </data>  
         <data name="total_parsimony_tree" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: parsimony tree">

diff --git a/tools/usher/usher.xml b/tools/usher/usher.xml
@@ -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">