comparison pm_dftb_opt.xml @ 2:6a99165bb7ca draft

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_dftb_opt commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507

1:23cb25b1d776

<tool id="pm_dftb_opt" name="PyMuonSuite AIRSS DFTB+ Optimise" version="0.1.1" python_template_version="3.5" profile="22.01">
    <description>run DFTB+ optimisation</description>
    <macros>
        <!-- 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}},
                license = {GPL-3.0},
                title = {{pymuon-suite}},
                url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
                version = {v0.2.1},
                month = {2},
                year = {2022},
                doi = {}
            }
        </token>
    </macros>
    <creator>
        <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>

        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
    </creator>
    <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="3.0">zip</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="get_out_folder.py"/>
        <include type="literal" path="run.sh"/>
        <include type="prefix" path="README-"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        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 ${__tool_directory__}/run.sh \$out_folder ;
        passed=$? &&
        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;
        zip -r dftb_results.zip \$out_folder params.yaml input_structure.* &&
        find \$out_folder > tree.txt
    ]]></command>
    <inputs>
        <param type="data" name="muonated_structures" label="Muonated structures (.zip)" format="zip" help="A zip folder containing muonated structures, as generated by the 'Generate muonated structures' tool or pm-muairss."/>

        </test>
    </tests>
    <help><![CDATA[
        usage: dftb+
        Given some input muonated structures (structures containing a muon), applies DFTB+ optimization to refine them.

        **LICENSE**

        All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
        International License. The full text of the license can be found at:

    ]]></help>
    <citations>
        <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>
    </citations>
</tool>

2:6a99165bb7ca

<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{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>
    </macros>
    <creator>
        <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>

        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
    </creator>
    <requirements>
        <!-- note versioning is different due to multiple dependencies -->
        <requirement type="package" version="21.2">dftbplus</requirement>
        <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
        <requirement type="package" version="3.0">zip</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="get_out_folder.py"/>
        <include type="literal" path="run.sh"/>
        <include type="prefix" path="README-"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        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 '${__tool_directory__}/run.sh' \$out_folder ;
        passed=$? &&
        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;
        zip -r dftb_results.zip \$out_folder params.yaml input_structure.* &&
        find \$out_folder > tree.txt
    ]]></command>
    <inputs>
        <param type="data" name="muonated_structures" label="Muonated structures (.zip)" format="zip" help="A zip folder containing muonated structures, as generated by the 'Generate muonated structures' tool or pm-muairss."/>

        </test>
    </tests>
    <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**

        All data is licensed under the Creative Commons Attribution-ShareAlike 4.0
        International License. The full text of the license can be found at:

    ]]></help>
    <citations>
        <citation type="bibtex">
            @PYMUONSUITE_CITATION@
        </citation>
        <citation type="doi">10.1063/1.5143190</citation>
    </citations>
</tool>