--- a/muon_macros.xml	Fri Feb 03 15:39:17 2023 +0000
+++ b/muon_macros.xml	Tue Jul 18 13:26:32 2023 +0000
@@ -17,4 +17,13 @@
             <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator>
         </param>
     </xml>
+    <!-- version of underlying tool (PEP 440) -->
+    <!-- citation should be updated with every underlying tool version -->
+    <!-- concept is not updated, and should only be used for referencing the idea of the software -->
+    <token name="@MUSPINSIM_VERSION@">2.2.1</token>
+    <token name="@MUSPINSIM_CITATION@">10.5281/zenodo.7733979</token>
+    <token name="@MUSPINSIM_CONCEPT@">10.5281/zenodo.6517626</token>
+    <token name="@PYMUONSUITE_VERSION@">0.3.0</token>
+    <token name="@PYMUONSUITE_CITATION@">10.5281/zenodo.8026711</token>
+    <token name="@PYMUONSUITE_CONCEPT@">10.5281/zenodo.7025643</token>
 </macros>
\ No newline at end of file

--- a/pm_asephonons.xml	Fri Feb 03 15:39:17 2023 +0000
+++ b/pm_asephonons.xml	Tue Jul 18 13:26:32 2023 +0000
@@ -1,24 +1,8 @@
-<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
+<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
     <description>calculate phonons using ASE and DFTB+</description>
     <macros>
-        <!-- version of underlying tool (PEP 440) -->
-        <token name="@TOOL_VERSION@">0.2.3</token>
         <!-- version of this tool wrapper (integer) -->
         <token name="@WRAPPER_VERSION@">0</token>
-        <!-- citation should be updated with every underlying tool version -->
-        <!-- typical fields to update are version, month, year, and doi -->
-        <token name="@PYMUONSUITE_CITATION@">
-            @software{Sturniolo_pymuon-suite_2022,
-                author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
-                license = {GPL-3.0},
-                month = {8},
-                title = {{pymuon-suite}},
-                url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
-                version = {v0.2.3},
-                doi = {10.5281/zenodo.7025644},
-                year = {2022}
-            }
-        </token>
         <import>muon_macros.xml</import>
     </macros>
     <creator>
@@ -28,7 +12,7 @@
     </creator>
     <requirements>
         <!-- note versioning is different due to multiple dependencies -->
-        <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
+        <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
         <requirement type="package" version="21.2">dftbplus</requirement>
         <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 -->
         <requirement type="package" version="3.0">zip</requirement>
@@ -188,9 +172,7 @@
         |
     ]]></help>
     <citations>
-        <citation type="bibtex">
-            @PYMUONSUITE_CITATION@
-        </citation>
+        <citation type="doi">@PYMUONSUITE_CITATION@</citation>
         <citation type="doi">10.1063/1.5085197</citation>
         <citation type="bibtex">
             @article{larsen2017atomic,