diff --git a/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml b/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
index 2d6fabbea3..80d9f9cd2e 100644
--- a/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
+++ b/chemicaltoolbox/openbabel/change_title_to_metadata_value.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/distance_finder.xml b/chemicaltoolbox/openbabel/distance_finder.xml
index 01dbae2c8b..365abaff36 100644
--- a/chemicaltoolbox/openbabel/distance_finder.xml
+++ b/chemicaltoolbox/openbabel/distance_finder.xml
@@ -2,7 +2,7 @@
     <description>- determine the minimum distances between a molecule and a set of 3D points</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/macros.xml b/chemicaltoolbox/openbabel/macros.xml
index ddd858483d..8b83241523 100644
--- a/chemicaltoolbox/openbabel/macros.xml
+++ b/chemicaltoolbox/openbabel/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@TOOL_VERSION@">3.2.1</token>
 
     <xml name="requirements">
         <requirements>
diff --git a/chemicaltoolbox/openbabel/ob_addh.xml b/chemicaltoolbox/openbabel/ob_addh.xml
index 876109a577..5079d7393a 100644
--- a/chemicaltoolbox/openbabel/ob_addh.xml
+++ b/chemicaltoolbox/openbabel/ob_addh.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_convert.xml b/chemicaltoolbox/openbabel/ob_convert.xml
index 4cc11cd5b8..0fcb5f9418 100644
--- a/chemicaltoolbox/openbabel/ob_convert.xml
+++ b/chemicaltoolbox/openbabel/ob_convert.xml
@@ -6,7 +6,7 @@
     -->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_depiction_svg.xml b/chemicaltoolbox/openbabel/ob_depiction_svg.xml
index 33357a9765..9204ba5251 100644
--- a/chemicaltoolbox/openbabel/ob_depiction_svg.xml
+++ b/chemicaltoolbox/openbabel/ob_depiction_svg.xml
@@ -2,7 +2,7 @@
     <description>of compounds</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_filter.xml b/chemicaltoolbox/openbabel/ob_filter.xml
index 24672c9f6b..9d2c604854 100644
--- a/chemicaltoolbox/openbabel/ob_filter.xml
+++ b/chemicaltoolbox/openbabel/ob_filter.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_genProp.xml b/chemicaltoolbox/openbabel/ob_genProp.xml
index 61096543d4..968f41ece8 100644
--- a/chemicaltoolbox/openbabel/ob_genProp.xml
+++ b/chemicaltoolbox/openbabel/ob_genProp.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_grep.xml b/chemicaltoolbox/openbabel/ob_grep.xml
index 97e020f445..56d6346d23 100644
--- a/chemicaltoolbox/openbabel/ob_grep.xml
+++ b/chemicaltoolbox/openbabel/ob_grep.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <options sanitize="False"/>
     <expand macro="requirements"/>
diff --git a/chemicaltoolbox/openbabel/ob_prepare_ligands.xml b/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
index fbd5f7b9e3..c6fb54e6ee 100644
--- a/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
+++ b/chemicaltoolbox/openbabel/ob_prepare_ligands.xml
@@ -2,7 +2,7 @@
     <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
diff --git a/chemicaltoolbox/openbabel/ob_remDuplicates.xml b/chemicaltoolbox/openbabel/ob_remDuplicates.xml
index 6782cf5c87..7ff655ab32 100644
--- a/chemicaltoolbox/openbabel/ob_remDuplicates.xml
+++ b/chemicaltoolbox/openbabel/ob_remDuplicates.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_remIons.xml b/chemicaltoolbox/openbabel/ob_remIons.xml
index e0fe46b539..bb9b7eccae 100644
--- a/chemicaltoolbox/openbabel/ob_remIons.xml
+++ b/chemicaltoolbox/openbabel/ob_remIons.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">3</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/ob_remSmall.xml b/chemicaltoolbox/openbabel/ob_remSmall.xml
index 8a91b0a2a7..71c0a834b3 100644
--- a/chemicaltoolbox/openbabel/ob_remSmall.xml
+++ b/chemicaltoolbox/openbabel/ob_remSmall.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
diff --git a/chemicaltoolbox/openbabel/ob_spectrophore_search.xml b/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
index 37b7a2135e..ab9e52ac3a 100644
--- a/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
+++ b/chemicaltoolbox/openbabel/ob_spectrophore_search.xml
@@ -2,10 +2,10 @@
     <description>- similarity search based on 1D chemical features</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.19.1">numpy</requirement>
+        <requirement type="package" version="2.5.2">numpy</requirement>
     </expand>
     <required_files>
         <include path="ob_spectrophore_search.py"/>
diff --git a/chemicaltoolbox/openbabel/remove_protonation_state.xml b/chemicaltoolbox/openbabel/remove_protonation_state.xml
index 3396bd8e82..a2ff381a97 100644
--- a/chemicaltoolbox/openbabel/remove_protonation_state.xml
+++ b/chemicaltoolbox/openbabel/remove_protonation_state.xml
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
diff --git a/chemicaltoolbox/openbabel/subsearch.xml b/chemicaltoolbox/openbabel/subsearch.xml
index 53feaa8f72..d5f7a9fa18 100644
--- a/chemicaltoolbox/openbabel/subsearch.xml
+++ b/chemicaltoolbox/openbabel/subsearch.xml
@@ -2,7 +2,7 @@
     <description>of fingerprint data sets</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>