# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1675438769 0
# Node ID 276a25ab05f26f2223d9c9aff5080b391cd63bdb
# Parent  eb6382889b9218ece7e2c63d52059a1c3bbca858
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_muairss_read commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

diff -r eb6382889b92 -r 276a25ab05f2 pm_muairss_read.xml
--- a/pm_muairss_read.xml	Thu Sep 15 10:25:00 2022 +0000
+++ b/pm_muairss_read.xml	Fri Feb 03 15:39:29 2023 +0000
@@ -1,22 +1,22 @@
-<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
+<tool id="pm_muairss_read" name="PyMuonSuite AIRSS Cluster" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
     <description>run clustering for optimised structures</description>
     <macros>
         <!-- version of underlying tool (PEP 440) -->
-        <token name="@TOOL_VERSION@">0.2.1</token>
+        <token name="@TOOL_VERSION@">0.2.3</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">1</token>
+        <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{pymuon-suite,
-                author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},
+            @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 = {v0.2.1},
-                month = {2},
-                year = {2022},
-                doi = {}
+                version = {v0.2.3},
+                doi = {10.5281/zenodo.7025644},
+                year = {2022}
             }
         </token>
     </macros>
@@ -32,18 +32,18 @@
         <include type="literal" path="get_out_folder.py"/>
     </required_files>
     <command detect_errors="exit_code"><![CDATA[
-        unzip "$optimisation_results" &&
+        unzip '$optimisation_results' &&
         if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
         && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
-        && out_folder="`python ${__tool_directory__}/get_out_folder.py`" &&
+        && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" &&
         pm-muairss -t r input_structure.* params.yaml
     ]]></command>
     <inputs>
         <param type="data" name="optimisation_results" label="optimised muonated structures (.zip)" format="zip" help="A zip folder containing a set of optimised muonated structures, the original structure, and a YAML parameter file. See below for the expected folder structure."/>
     </inputs>
     <outputs>
-        <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="$out_folder/*clusters.txt"/>
-        <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="$out_folder/*clusters.dat"/>
+        <data label="Cluster report for $optimisation_results.name" name="cluster_report" format="txt" from_work_dir="${out_folder}/*clusters.txt"/>
+        <data label="Cluster data for $optimisation_results.name" name="cluster_data" format="txt" from_work_dir="${out_folder}/*clusters.dat"/>
     </outputs>
     <tests>
         <test expect_num_outputs="2">
@@ -88,65 +88,16 @@
         'Generate muon structures' tool or pm-muairss.
 
         Command-line usage: pm-muairss [-h] -t r structures parameter_file
+
+        PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
     ]]></help>
     <citations>
         <citation type="bibtex">
             @TOOL_CITATION@
         </citation>
-        <citation type="bibtex">
-            @article{airss,
-                author = {Liborio, L. and Sturniolo, S. and Jochym, D.},
-                title = {Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)},
-                journal = {The Journal of Chemical Physics},
-                volume = {148},
-                pages = {134114},
-                year = {2018},
-                doi={10.1063/1.5024450},
-                URL={
-                    https://doi.org/10.1063/1.5024450
-                },
-                eprint={
-                    https://doi.org/10.1063/1.5024450
-                }
-            }
-        </citation>
-        <citation type="bibtex">
-            @article{doi:10.1063/1.5085197,
-                author = {Sturniolo,Simone  and Liborio,Leandro  and Jackson,Samuel },
-                title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},
-                journal = {The Journal of Chemical Physics},
-                volume = {150},
-                number = {15},
-                pages = {154301},
-                year = {2019},
-                doi = {10.1063/1.5085197},
-                URL = {
-                        https://doi.org/10.1063/1.5085197
-                },
-                eprint = {
-                        https://doi.org/10.1063/1.5085197
-                }
-            }
-        </citation>
-        <citation type="bibtex">
-            @article{doi:10.1063/5.0012381,
-                author = {Sturniolo,Simone  and Liborio,Leandro },
-                title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},
-                journal = {The Journal of Chemical Physics},
-                volume = {153},
-                number = {4},
-                pages = {044111},
-                year = {2020},
-                doi = {10.1063/5.0012381},
-                URL = {
-                        https://doi.org/10.1063/5.0012381
-                },
-                eprint = {
-                        https://doi.org/10.1063/5.0012381
-                },
-                abstract = { Finding the stopping site of the muon in a muon-spin relaxation experiment is one of the main problems of muon spectroscopy, and computational techniques that make use of quantum chemistry simulations can be of great help when looking for this stopping site. The most thorough approach would require the use of simulations, such as Density Functional Theory (DFT), to test and optimise multiple possible sites, accounting for the effect that the added muon has on its surroundings. However, this can be computationally expensive and sometimes unnecessary. Hence, in this work, we present a software implementation of the Unperturbed Electrostatic Potential (UEP) Method: an approach used for finding the muon stopping site in crystalline materials. The UEP method requires only one DFT calculation, necessary to compute the electronic density. This, in turn, is used to calculate the minima of the crystalline material’s electrostatic potential and the estimates of the muon stopping site, relying on the approximation that the muon’s presence does not significantly affect its surroundings. One of the main UEP’s assumptions is that the muon stopping site will be one of the crystalline material’s electrostatic potential minima. In this regard, we also propose some symmetry-based considerations about the properties of this crystalline material’s electrostatic potential, in particular, which sites are more likely to be its minima and why the unperturbed approximation may be sufficiently robust for them. We introduce the Python software package pymuon-suite and the various utilities it provides to facilitate these calculations, and finally, we demonstrate the effectiveness of the method with some chosen example systems. }
-            }
-        </citation>
+        <citation type="doi">10.1063/1.5024450</citation>
+        <citation type="doi">10.1063/1.5085197</citation>
+        <citation type="doi">10.1063/5.0012381</citation>
         <citation type="bibtex">
             @article {castep,
                 author = {Clark, S. J. and Segall, M. D. and Pickard, C. J. and Hasnip, P. J. and Probert, M. I. J. and Refson, K. and Payne, M. C.},