From aa7c7a35834f36dad6e72d5f54089a578be60731 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <bebatut@gmail.com>
Date: Thu, 2 Nov 2023 15:50:10 +0100
Subject: [PATCH] Replace EDAM by biotools for instrain (#5575)

---
 tools/instrain/.shed.yml            |  2 +-
 tools/instrain/instrain_compare.xml |  2 +-
 tools/instrain/instrain_profile.xml |  2 +-
 tools/instrain/macros.xml           | 14 ++++----------
 4 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/tools/instrain/.shed.yml b/tools/instrain/.shed.yml
index 879d45a0a5b..7a9651c7697 100644
--- 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
index 39572b8eb14..5d33af6e556 100644
--- 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
index 88f63d656ff..f6517c32e84 100644
--- 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
index 94bbb029af0..598d9b4495d 100644
--- 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>