diff --git a/tools/mdanalysis/extract_rmsd.xml b/tools/mdanalysis/extract_rmsd.xml
index adc53407..ea218e59 100644
--- a/tools/mdanalysis/extract_rmsd.xml
+++ b/tools/mdanalysis/extract_rmsd.xml
@@ -2,7 +2,7 @@
     <description>from MD ensemble with MDAnalysis</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="exit_code"><![CDATA[
diff --git a/tools/mdanalysis/macros.xml b/tools/mdanalysis/macros.xml
index 53f31b59..0db3118a 100644
--- a/tools/mdanalysis/macros.xml
+++ b/tools/mdanalysis/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@TOOL_VERSION@">2.8.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">mdanalysis</requirement>
diff --git a/tools/mdanalysis/ramachandran_auto_protein.xml b/tools/mdanalysis/ramachandran_auto_protein.xml
index 15d235b5..39154eef 100644
--- a/tools/mdanalysis/ramachandran_auto_protein.xml
+++ b/tools/mdanalysis/ramachandran_auto_protein.xml
@@ -5,9 +5,9 @@
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.10.0">seaborn</requirement>
-        <requirement type="package" version="2.10.0">h5py</requirement>
-        <requirement type="package" version="2.11.1">jinja2</requirement>
+        <requirement type="package" version="0.13.2">seaborn</requirement>
+        <requirement type="package" version="3.12.1">h5py</requirement>
+        <requirement type="package" version="3.1.5">jinja2</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/ramachandran_auto_protein.py'
diff --git a/tools/mdanalysis/ramachandran_plots.xml b/tools/mdanalysis/ramachandran_plots.xml
index e3e8d130..ff67f04d 100644
--- a/tools/mdanalysis/ramachandran_plots.xml
+++ b/tools/mdanalysis/ramachandran_plots.xml
@@ -5,10 +5,10 @@
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.5.2">scipy</requirement>
-        <requirement type="package" version="0.10.0">seaborn</requirement>
-        <requirement type="package" version="2.0.0">nbdime</requirement>
-        <requirement type="package" version="5.3.1">pyyaml</requirement>
+        <requirement type="package" version="1.14.1">scipy</requirement>
+        <requirement type="package" version="0.13.2">seaborn</requirement>
+        <requirement type="package" version="4.0.2">nbdime</requirement>
+        <requirement type="package" version="6.0.2">pyyaml</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/ramachandran_plots.py'