From 526030bc7a8af67cd2eb2d7607cfb07d19e5d0b4 Mon Sep 17 00:00:00 2001
From: Zargham Ahmad <zargham.ahmad12@gmail.com>
Date: Fri, 20 Oct 2023 17:13:55 +0200
Subject: [PATCH] Added xref to bio.tools for retip and msfinder

---
 tools/recetox_msfinder/macros.xml           | 5 +++++
 tools/recetox_msfinder/recetox_msfinder.xml | 3 ++-
 tools/retip/macros.xml                      | 6 ++++++
 tools/retip/retip_apply.xml                 | 3 ++-
 tools/retip/retip_descriptors.xml           | 3 ++-
 tools/retip/retip_filter_rt.xml             | 3 ++-
 tools/retip/retip_train.xml                 | 3 ++-
 7 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/tools/recetox_msfinder/macros.xml b/tools/recetox_msfinder/macros.xml
index f4727119..651dfda9 100644
--- a/tools/recetox_msfinder/macros.xml
+++ b/tools/recetox_msfinder/macros.xml
@@ -18,6 +18,11 @@
                 name="RECETOX MUNI" />
         </creator>
     </xml>
+    <xml name="refs">
+        <xrefs>
+               <xref type="bio.tools">recetox-msfinder</xref>
+        </xrefs>
+     </xml>
     <xml name="input">
         <param name="input_data" type="data" format="msp" label="Input mass spectral library file to which to add peak annotations."
             help="Formula and InChI (or SMILES) codes are required to be present in the library file" />
diff --git a/tools/recetox_msfinder/recetox_msfinder.xml b/tools/recetox_msfinder/recetox_msfinder.xml
index b065572c..3bf859f2 100644
--- a/tools/recetox_msfinder/recetox_msfinder.xml
+++ b/tools/recetox_msfinder/recetox_msfinder.xml
@@ -1,8 +1,9 @@
-<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy1">
+<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy2">
     <description>Annotation of fragment peaks in mass spectral libraries.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="refs"/>
     <expand macro="creator" />
 
     <expand macro="requirements" />
diff --git a/tools/retip/macros.xml b/tools/retip/macros.xml
index c1301248..af9c5456 100644
--- a/tools/retip/macros.xml
+++ b/tools/retip/macros.xml
@@ -20,6 +20,12 @@
         </creator>
     </xml>
 
+    <xml name="refs">
+        <xrefs>
+               <xref type="bio.tools">retip</xref>
+        </xrefs>
+     </xml>
+
     <xml name="requirements">
         <requirements>
             <container type="docker">recetox/retip:@TOOL_VERSION@-recetox4</container>
diff --git a/tools/retip/retip_apply.xml b/tools/retip/retip_apply.xml
index 7125a8dc..f151201a 100644
--- a/tools/retip/retip_apply.xml
+++ b/tools/retip/retip_apply.xml
@@ -1,8 +1,9 @@
-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy4">
+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy5">
     <description>is retention time predictor for Metabolomics</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <expand macro="requirements"/>
diff --git a/tools/retip/retip_descriptors.xml b/tools/retip/retip_descriptors.xml
index 9973282b..f723f996 100644
--- a/tools/retip/retip_descriptors.xml
+++ b/tools/retip/retip_descriptors.xml
@@ -1,8 +1,9 @@
-<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy4">
+<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy5">
     <description>for retention time prediction</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <expand macro="requirements"/>
diff --git a/tools/retip/retip_filter_rt.xml b/tools/retip/retip_filter_rt.xml
index f994f1ff..1f83e0ab 100644
--- a/tools/retip/retip_filter_rt.xml
+++ b/tools/retip/retip_filter_rt.xml
@@ -1,8 +1,9 @@
-<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy4">
+<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy5">
     <description>for predicted RT's</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <expand macro="requirements"/>
diff --git a/tools/retip/retip_train.xml b/tools/retip/retip_train.xml
index 4b1affdd..5f55224b 100644
--- a/tools/retip/retip_train.xml
+++ b/tools/retip/retip_train.xml
@@ -1,8 +1,9 @@
-<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy4">
+<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy5">
     <description>the Keras model to predict retention times</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="refs"/>
     <expand macro="creator"/>
 
     <expand macro="requirements"/>