From a70988758e7ec77efad404b7e3ed48c3f982a979 Mon Sep 17 00:00:00 2001
From: paulzierep <paul.zierep@googlemail.com>
Date: Thu, 7 Mar 2024 09:37:01 +0100
Subject: [PATCH] Add bio.tools xref to ete tools

---
 tools/ete/ete_gene_cnv.xml               | 1 +
 tools/ete/ete_genetree_splitter.xml      | 1 +
 tools/ete/ete_homology_classifier.xml    | 1 +
 tools/ete/ete_init_taxdb.xml             | 1 +
 tools/ete/ete_lineage_generator.xml      | 1 +
 tools/ete/ete_macros.xml                 | 5 +++++
 tools/ete/ete_mod.xml                    | 1 +
 tools/ete/ete_species_tree_generator.xml | 1 +
 8 files changed, 12 insertions(+)

diff --git a/tools/ete/ete_gene_cnv.xml b/tools/ete/ete_gene_cnv.xml
index a5ce2fce..d4191863 100644
--- a/tools/ete/ete_gene_cnv.xml
+++ b/tools/ete/ete_gene_cnv.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/ete_gene_cnv.py'
diff --git a/tools/ete/ete_genetree_splitter.xml b/tools/ete/ete_genetree_splitter.xml
index 9ef83a76..4c906dce 100644
--- a/tools/ete/ete_genetree_splitter.xml
+++ b/tools/ete/ete_genetree_splitter.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <stdio>
         <!-- Anything other than zero is an error -->
diff --git a/tools/ete/ete_homology_classifier.xml b/tools/ete/ete_homology_classifier.xml
index 102ffa02..ef9ae36e 100644
--- a/tools/ete/ete_homology_classifier.xml
+++ b/tools/ete/ete_homology_classifier.xml
@@ -12,6 +12,7 @@
             </param>
         </xml>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code">
     <![CDATA[
diff --git a/tools/ete/ete_init_taxdb.xml b/tools/ete/ete_init_taxdb.xml
index e679548f..481f1d98 100644
--- a/tools/ete/ete_init_taxdb.xml
+++ b/tools/ete/ete_init_taxdb.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/ete_init_taxdb.py'
diff --git a/tools/ete/ete_lineage_generator.xml b/tools/ete/ete_lineage_generator.xml
index a2095039..ac60f15e 100644
--- a/tools/ete/ete_lineage_generator.xml
+++ b/tools/ete/ete_lineage_generator.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/ete_lineage_generator.py'
diff --git a/tools/ete/ete_macros.xml b/tools/ete/ete_macros.xml
index 12735336..9e7c1f2c 100644
--- a/tools/ete/ete_macros.xml
+++ b/tools/ete/ete_macros.xml
@@ -1,6 +1,11 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@VERSION@">3.1.2</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">ete</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">ete3</requirement>
diff --git a/tools/ete/ete_mod.xml b/tools/ete/ete_mod.xml
index dcd03e60..7b67bcdf 100644
--- a/tools/ete/ete_mod.xml
+++ b/tools/ete/ete_mod.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 ete3 mod -t
diff --git a/tools/ete/ete_species_tree_generator.xml b/tools/ete/ete_species_tree_generator.xml
index 10d0bcc8..10f09515 100644
--- a/tools/ete/ete_species_tree_generator.xml
+++ b/tools/ete/ete_species_tree_generator.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ete_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <stdio>
         <!-- Anything other than zero is an error -->