From 98b63a2738094b3841420bd399e487bdbc41c8b9 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Thu, 25 Jul 2024 14:31:47 +0200
Subject: [PATCH 1/2] Checked  EDAM annotations for QCxMS and xTB tools

---
 tools/qcxms/macros.xml                   | 2 +-
 tools/xtb/macros.xml                     | 8 ++++++++
 tools/xtb/xtb_molecular_optimization.xml | 3 ++-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/tools/qcxms/macros.xml b/tools/qcxms/macros.xml
index fc4f5b2c..ae82c531 100644
--- a/tools/qcxms/macros.xml
+++ b/tools/qcxms/macros.xml
@@ -10,7 +10,7 @@
             <edam_topic>topic_3332</edam_topic>
         </edam_topics>
         <edam_operations>
-            <edam_operation>operation_0297</edam_operation>
+            <edam_operation>operation_3860</edam_operation>
         </edam_operations>
     </xml>
 
diff --git a/tools/xtb/macros.xml b/tools/xtb/macros.xml
index 96b5d133..10ca62fc 100644
--- a/tools/xtb/macros.xml
+++ b/tools/xtb/macros.xml
@@ -1,5 +1,13 @@
 <macros>
     <token name="@TOOL_VERSION@">6.6.1</token>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_3332</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0297</edam_operation>
+        </edam_operations>
+    </xml>
     <xml name="creator">
     <creator>
         <person
diff --git a/tools/xtb/xtb_molecular_optimization.xml b/tools/xtb/xtb_molecular_optimization.xml
index 13951ccb..859d8fd0 100644
--- a/tools/xtb/xtb_molecular_optimization.xml
+++ b/tools/xtb/xtb_molecular_optimization.xml
@@ -1,8 +1,9 @@
-<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>Semiempirical quantum mechanical molecular optimization method</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="edam"/>
     <expand macro="creator"/>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">xtb</requirement>

From 5b18854de6b5ca41109c31e923f98d83d273e372 Mon Sep 17 00:00:00 2001
From: wverastegui <wudmir.rojas@recetox.muni.cz>
Date: Thu, 25 Jul 2024 15:22:06 +0200
Subject: [PATCH 2/2] Updated galaxy wrapper versions

---
 tools/qcxms/qcxms_getres.xml      | 2 +-
 tools/qcxms/qcxms_neutral_run.xml | 2 +-
 tools/qcxms/qcxms_prod_run.xml    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/qcxms/qcxms_getres.xml b/tools/qcxms/qcxms_getres.xml
index a2848add..6bce00af 100644
--- a/tools/qcxms/qcxms_getres.xml
+++ b/tools/qcxms/qcxms_getres.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy1" profile="22.09">
+<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy2" profile="22.09">
     <description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>
diff --git a/tools/qcxms/qcxms_neutral_run.xml b/tools/qcxms/qcxms_neutral_run.xml
index 3b7a86de..5dd74f8f 100644
--- a/tools/qcxms/qcxms_neutral_run.xml
+++ b/tools/qcxms/qcxms_neutral_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy3" profile="22.09">
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy4" profile="22.09">
     <description>required as first step to prepare for the production runs</description>
     
     <macros>
diff --git a/tools/qcxms/qcxms_prod_run.xml b/tools/qcxms/qcxms_prod_run.xml
index 634f735f..a8ba0263 100644
--- a/tools/qcxms/qcxms_prod_run.xml
+++ b/tools/qcxms/qcxms_prod_run.xml
@@ -1,4 +1,4 @@
-<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy2" profile="22.09">
+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy3" profile="22.09">
     <description>Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>