changeset 3:e002cee8f707 draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/muspinsim commit 70a4d37ecdf5d586703cfc509922311e95d3205c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muon_macros.xml	Tue Jul 18 13:25:55 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

--- a/muspinsim.xml	Fri Feb 03 15:39:01 2023 +0000
+++ b/muspinsim.xml	Tue Jul 18 13:25:55 2023 +0000
@@ -1,24 +1,9 @@
-<tool id="muspinsim" name="MuSpinSim Simulate" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
+<tool id="muspinsim" name="MuSpinSim Simulate" version="@MUSPINSIM_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
     <description>perform spin dynamics calculations for muon science experiments</description>
     <macros>
-        <!-- version of underlying tool (PEP 440) -->
-        <token name="@TOOL_VERSION@">2.0.2</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="@TOOL_CITATION@">
-            @software{muspinsim,
-                author = {Sturniolo, Simone and Liborio, Leandro and Owen, Josh and Mudaraddi, Anish and Davies, Joel and Wilkinson, John and {Muon Spectroscopy Computational Project}},
-                license = {MIT},
-                title = {{muspinsim}},
-                url = {https://github.com/muon-spectroscopy-computational-project/muspinsim},
-                version = {v2.0.2},
-                month = {1},
-                year = {2023}
-                doi = {10.5281/zenodo.7568830}
-            }
-        </token>
+        <import>muon_macros.xml</import>
     </macros>
     <creator>
         <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
@@ -27,7 +12,7 @@
         <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
     </creator>
     <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">muspinsim</requirement>
+        <requirement type="package" version="@MUSPINSIM_VERSION@">muspinsim</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ## remove spaces in names
@@ -154,8 +139,6 @@
         Command-line usage: muspinsim muspinsim.in
     ]]></help>
     <citations>
-        <citation type="bibtex">
-            @TOOL_CITATION@
-        </citation>
+        <citation type="doi">@MUSPINSIM_CITATION@</citation>
     </citations>
 </tool>