From 951dcdf06969a67ae7761e7380b8600d16f90fb1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Fri, 23 Feb 2024 16:19:11 +0100
Subject: [PATCH 1/2] Add bio.tools for mob_suite

---
 tools/mob_suite/macros.xml    | 11 ++++++++---
 tools/mob_suite/mob_recon.xml |  3 ++-
 tools/mob_suite/mob_typer.xml |  1 +
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/tools/mob_suite/macros.xml b/tools/mob_suite/macros.xml
index f0def59c..a722904b 100644
--- a/tools/mob_suite/macros.xml
+++ b/tools/mob_suite/macros.xml
@@ -1,8 +1,13 @@
 <macros>
   <token name="@VERSION@">3.0.3</token>
+  <xml name="bio_tools">
+    <xrefs>
+      <xref type="bio.tools">mob_suite</xref>
+    </xrefs>
+  </xml>
   <xml name="requirements">
-  <requirements>
-  <requirement type="package" version ="@VERSION@">mob_suite</requirement>
-  </requirements>
+    <requirements>
+      <requirement type="package" version ="@VERSION@">mob_suite</requirement>
+    </requirements>
   </xml>
 </macros>
diff --git a/tools/mob_suite/mob_recon.xml b/tools/mob_suite/mob_recon.xml
index d974f909..1c3fcffb 100644
--- a/tools/mob_suite/mob_recon.xml
+++ b/tools/mob_suite/mob_recon.xml
@@ -2,7 +2,8 @@
   <description>Type contigs and extract plasmid sequences</description>
   <macros>
     <import>macros.xml</import>
-  </macros>  
+  </macros>
+  <expand macro="bio_tools"/>
   <expand macro="requirements" />
   <version_command>mob_recon --version</version_command>
   <command detect_errors="exit_code">
diff --git a/tools/mob_suite/mob_typer.xml b/tools/mob_suite/mob_typer.xml
index 16dcf601..7d5bbfa6 100644
--- a/tools/mob_suite/mob_typer.xml
+++ b/tools/mob_suite/mob_typer.xml
@@ -3,6 +3,7 @@
   <macros>
     <import>macros.xml</import>
   </macros>
+  <expand macro="bio_tools"/>
   <expand macro="requirements"/>
   <version_command>mob_typer --version</version_command>
   <command detect_errors="exit_code">

From f794fa33faadf850a6d2bfdaadc51dd0389f9b69 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Fri, 23 Feb 2024 16:19:29 +0100
Subject: [PATCH 2/2] Fix link to remote_repository_url

---
 tools/mob_suite/.shed.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mob_suite/.shed.yml b/tools/mob_suite/.shed.yml
index 654bb32e..55fd83c7 100644
--- a/tools/mob_suite/.shed.yml
+++ b/tools/mob_suite/.shed.yml
@@ -3,5 +3,5 @@ description: MOB-suite is a set of software tools for clustering, reconstruction
 name: mob_suite
 owner: nml
 long_description: The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies designed  by Robertson James et al.
-remote_repository_url: https://github.com/phac-nml/mob-suite
+remote_repository_url: https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite
 homepage_url: https://github.com/phac-nml/mob-suite