Replace EDAM by biotools for instrain (#5575)

galaxyproject · Nov 2, 2023 · aa7c7a3 · aa7c7a3
1 parent 3973ed2
commit aa7c7a3
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Showing 4 changed files with 7 additions and 13 deletions.
diff --git a/tools/instrain/.shed.yml b/tools/instrain/.shed.yml
@@ -7,7 +7,7 @@ long_description: |
      metagenomes that allows highly accurate genome comparisons, analysis of coverage,
      microdiversity, and linkage, and sensitive SNP detection with gene localization and
      synonymous non-synonymous identification.
-remote_repository_url: https://github.com/MrOlm/inStrain
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain
 type: unrestricted
 categories:
 - Metagenomics

diff --git a/tools/instrain/instrain_compare.xml b/tools/instrain/instrain_compare.xml
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="edam_ontology"/>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <version_command>inStrain compare --version</version_command>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/instrain/instrain_profile.xml b/tools/instrain/instrain_profile.xml
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="edam_ontology"/>
+    <expand macro="biotools"/>
     <expand macro="requirements"/>
     <version_command>inStrain profile --version</version_command>
     <command detect_errors="exit_code"><![CDATA[

diff --git a/tools/instrain/macros.xml b/tools/instrain/macros.xml
@@ -3,16 +3,10 @@
     <token name="@TOOL_VERSION@">1.5.3</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.01</token>
-    <xml name="edam_ontology">
-        <edam_topics>
-            <edam_topic>topic_0102</edam_topic>
-            <edam_topic>topic_3174</edam_topic>
-        </edam_topics>
-        <edam_operations>
-            <edam_operation>operation_0484</edam_operation>
-            <edam_operation>operation_3209</edam_operation>           
-            <edam_operation>operation_3730</edam_operation>
-        </edam_operations>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">instrain</xref>
+        </xrefs>
     </xml>
     <xml name="requirements">
         <requirements>