# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1675438763 0
# Node ID 6a99165bb7ca8f97663f99d9955b4624dcab5f0c
# Parent  23cb25b1d776fb7cccff8f8ebc194ba35c472fc5
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_dftb_opt commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

diff -r 23cb25b1d776 -r 6a99165bb7ca pm_dftb_opt.xml
--- a/pm_dftb_opt.xml	Thu Sep 15 10:19:38 2022 +0000
+++ b/pm_dftb_opt.xml	Fri Feb 03 15:39:23 2023 +0000
@@ -1,18 +1,22 @@
-<tool id="pm_dftb_opt" name="PyMuonSuite AIRSS DFTB+ Optimise" version="0.1.1" python_template_version="3.5" profile="22.01">
+<tool id="pm_dftb_opt" name="PyMuonSuite AIRSS DFTB+ Optimise" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
     <description>run DFTB+ optimisation</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{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>
@@ -24,7 +28,7 @@
     <requirements>
         <!-- note versioning is different due to multiple dependencies -->
         <requirement type="package" version="21.2">dftbplus</requirement>
-        <requirement type="package" version="0.2.1">pymuonsuite</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
         <requirement type="package" version="3.0">zip</requirement>
     </requirements>
     <required_files>
@@ -33,15 +37,15 @@
         <include type="prefix" path="README-"/>
     </required_files>
     <command detect_errors="exit_code"><![CDATA[
-        unzip "$muonated_structures" &&
+        unzip '$muonated_structures' &&
         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`" ;
-        bash ${__tool_directory__}/run.sh \$out_folder ;
+        && out_folder="`python '${__tool_directory__}/get_out_folder.py'`" ;
+        bash '${__tool_directory__}/run.sh' \$out_folder ;
         passed=$? &&
         echo \$passed &&
         if [ \$passed == 2 ]; then echo "input file structure is not dftb" && exit 25; elif [ \$passed == 3 ]; then echo "error in parsing dftb file. check log for details" && exit 26; else echo "parse ok"; fi &&
-        if grep -q 'pbc-0-3' params.yaml; then cp ${__tool_directory__}/README-pbc \$out_folder/README; elif grep -q '3ob-3-1' params.yaml; then cp ${__tool_directory__}/README-3ob \$out_folder README; else ( cp ${__tool_directory__}/README-3ob \$out_folder README-3ob && cp ${__tool_directory__}/README-pbc \$out_folder/README-pbc ); fi;
+        if grep -q 'pbc-0-3' params.yaml; then cp '${__tool_directory__}/README-pbc' \$out_folder/README; elif grep -q '3ob-3-1' params.yaml; then cp '${__tool_directory__}/README-3ob' \$out_folder README; else ( cp '${__tool_directory__}/README-3ob' \$out_folder README-3ob && cp '${__tool_directory__}/README-pbc' \$out_folder/README-pbc ); fi;
         zip -r dftb_results.zip \$out_folder params.yaml input_structure.* &&
         find \$out_folder > tree.txt
     ]]></command>
@@ -70,6 +74,8 @@
     <help><![CDATA[
         usage: dftb+
         Given some input muonated structures (structures containing a muon), applies DFTB+ optimization to refine them.
+        
+        PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
 
         **LICENSE**
 
@@ -123,25 +129,6 @@
         <citation type="bibtex">
             @PYMUONSUITE_CITATION@
         </citation>
-        <citation type="bibtex">
-        @article{doi:10.1063/1.5143190,
-         author = {Hourahine,B.  and Aradi,B.  and Blum,V.  and Bonafé,F.  and Buccheri,A.  and Camacho,C.  and Cevallos,C.  and Deshaye,M. Y.  and Dumitrică,T.  and Dominguez,A.  and Ehlert,S.  and Elstner,M.  and van der Heide,T.  and Hermann,J.  and Irle,S.  and Kranz,J. J.  and Köhler,C.  and Kowalczyk,T.  and Kubař,T.  and Lee,I. S.  and Lutsker,V.  and Maurer,R. J.  and Min,S. K.  and Mitchell,I.  and Negre,C.  and Niehaus,T. A.  and Niklasson,A. M. N.  and Page,A. J.  and Pecchia,A.  and Penazzi,G.  and Persson,M. P.  and Řezáč,J.  and Sánchez,C. G.  and Sternberg,M.  and Stöhr,M.  and Stuckenberg,F.  and Tkatchenko,A.  and Yu,V. W.-z.  and Frauenheim,T. },
-         title = {DFTB+, a software package for efficient approximate density functional theory based atomistic simulations},
-         journal = {The Journal of Chemical Physics},
-         volume = {152},
-         number = {12},
-         pages = {124101},
-         year = {2020},
-         doi = {10.1063/1.5143190},
-
-         URL = {
-                 https://doi.org/10.1063/1.5143190
-
-         },
-         eprint = {
-                 https://doi.org/10.1063/1.5143190
-         }
-         }
-        </citation>
+        <citation type="doi">10.1063/1.5143190</citation>
     </citations>
 </tool>