# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1689686786 0
# Node ID e15e8800c39e66a8e4d339e53a31e5b9437c4b58
# Parent  d7a0a31760b144c4af2bb603fd2f158ebe0c118b
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim_plot commit 70a4d37ecdf5d586703cfc509922311e95d3205c

diff -r d7a0a31760b1 -r e15e8800c39e muon_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muon_macros.xml	Tue Jul 18 13:26:26 2023 +0000
@@ -0,0 +1,29 @@
+<macros>
+    <xml name="dftb_set">
+        <param type="select" name="dftb_set" value="3ob-3-1" display="radio" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details.">
+            <option value="3ob-3-1">3ob-3-1</option>
+            <option value="pbc-0-3">pbc-0-3</option>
+        </param>
+    </xml>
+    <xml name="dftb+">
+        <expand macro="dftb_set"/>
+        <param type="boolean" name="dftb_pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." checked="true"/>
+    </xml>
+    <xml name="dftb_optionals">
+        <param type="text" argument="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/>
+    </xml>
+    <xml name="k_points_grid">
+        <param type="text" argument="k_points_grid" value="[1,1,1]" label="K-points grid" help="List of three integer k-points. Default is [1,1,1].">
+            <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
diff -r d7a0a31760b1 -r e15e8800c39e muspinsim_plot.xml
--- a/muspinsim_plot.xml	Fri Feb 03 15:39:12 2023 +0000
+++ b/muspinsim_plot.xml	Tue Jul 18 13:26:26 2023 +0000
@@ -4,29 +4,16 @@
         <!-- version of underlying tool (PEP 440) -->
         <token name="@TOOL_VERSION@">3.5.1</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">2</token>
         <!-- citation should be updated with every underlying tool version -->
         <!-- typical fields to update are version, month, year, and doi -->
-        <token name="@TOOL_CITATION@">
-            @article{Hunter:2007,
-                author = {Hunter, J. D.},
-                title = {Matplotlib: A 2D graphics environment},
-                journal = {Computing in Science &amp; Engineering},
-                volume = {9},
-                number = {3},
-                pages = {90--95},
-                abstract = {Matplotlib is a 2D graphics package used for Python for
-                      application development, interactive scripting, and publication-quality
-                      image generation across user interfaces and operating systems.},
-                      publisher = {IEEE COMPUTER SOC},
-                doi = {10.1109/MCSE.2007.55},
-                year = {2007}
-            }
-        </token>
+        <token name="@TOOL_CITATION@">10.1109/MCSE.2007.55</token>
+        <import>muon_macros.xml</import>
     </macros>
     <creator>
         <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
         <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
+        <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
         <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
     </creator>
     <requirements>
@@ -82,10 +69,10 @@
         </repeat>
     </inputs>
     <outputs>
-        <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf">
+        <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf" label="PDF plot on ${on_string}">
             <filter>(out_file_type == 'pdf')</filter>
         </data>
-        <data format="png" name="out_file_png" from_work_dir="outfile.png">
+        <data format="png" name="out_file_png" from_work_dir="outfile.png" label="PNG plot on ${on_string}">
             <filter>(out_file_type == 'png')</filter>
         </data>
     </outputs>
@@ -147,20 +134,7 @@
         You can overlay multiple plots on top of each other by providing more than one data file.
     ]]></help>
     <citations>
-        <citation type="bibtex">
-            @TOOL_CITATION@
-        </citation>
-        <citation type="bibtex">
-            @software{muspinsim,
-                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
-                license = {MIT},
-                title = {{muspinsim}},
-                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
-                version = {v1.1.0},
-                month = {5},
-                year = {2022},
-                doi = {10.5281/zenodo.6563074}
-            }
-        </citation>
+        <citation type="doi">@TOOL_CITATION@</citation>
+        <citation type="doi">@MUSPINSIM_CONCEPT@</citation>
     </citations>
 </tool>