annotate pm_dftb_opt.xml @ 2:6a99165bb7ca draft default tip

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

<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"/>
        <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
        <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."/>
        <param type="hidden" name="testing" label="Test mode" value="false"/>
    </inputs>
    <outputs>
        <data label="DFTB results for $muonated_structures.name" name="dftb_results" format="zip" from_work_dir="dftb_results.zip"/>
        <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
            <filter>(testing == "true")</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="testing" value="true"/>
            <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
            <output name="file_tree" file="tree.txt" ftype="txt" sort="true"/>
        </test>
        <!-- check that file_tree filter works -->
        <test expect_num_outputs="1">
            <param name="testing" value="false"/>
            <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
        </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:

        https://creativecommons.org/licenses/by-sa/4.0/legalcode

        For specific data sets remember to cite the following papers, by element :

|        **3-ob-1**


+--------------+------------------------------------------------+-----------------------------------+------------------------------------+
| [JCTC2013]   | \ J. Chem. Theory Comput., 2013, 9, 338-354.   | (O, N, C, H)                      | https://doi.org/10.1021/ct300849w  |
+--------------+------------------------------------------------+-----------------------------------+------------------------------------+
| [JCTC2014]   | \ J. Chem. Theory Comput., 2014, 10, 1518-1537.| (P,S-\*)                          | https://doi.org/10.1021/ct401002w  |
+--------------+------------------------------------------------+-----------------------------------+------------------------------------+
| [JCTC2015-1] | \ J. Phys. Chem. B, 2015, 119, 1062-1082.      | (Mg,Zn-\*)                        | https://doi.org/10.1021/jp506557r  |
+--------------+------------------------------------------------+-----------------------------------+------------------------------------+
| [JCTC2015-2] | \ J. Chem. Theory Comput., 2015, 11, 332-342.  | (Na,F,K,Ca,Cl,Br,I-\*)            | https://doi.org/10.1021/ct5009137  |
+--------------+------------------------------------------------+-----------------------------------+------------------------------------+

|
|    **pbc-0-3**

+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
|   [SiC]    | \ E. Rauls, R. Gutierrez, J. Elsner, and Th. Frauenheim, Sol. State Comm. 111, 459 (1999)  | (Si-C)  | https://doi.org/10.1016/S0038-1098(99)00137-4  |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
|   [SiO]    | \ C. Koehler, Z. Hajnal, P. Deak, Th. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) |  (Si-O) | https://doi.org/10.1103/PhysRevB.64.085333     |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
| [Silicon]  | \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003).       |  (Si)   | https://doi.org/10.1002/pssb.200301886         |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
| [Fluorine] | \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006).                               | \ (F)   | https://doi.org/10.1016/j.susc.2005.10.044     |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
|   [Iron]   | \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005).                   |   (Fe)  | https://doi.org/10.1016/j.chemphys.2004.03.034 |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+
|   [SiSi]   | \ A. Sieck, PhD. Thesis, University of Paderborn, 2000.                                    | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635   |
+------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+

|
| The full sets and all other data can be found at the following URLs:

+----------+------------------------------------------------------------+
|  3-ob-1  |   https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ |
+----------+------------------------------------------------------------+
| pbc-0-3  |  https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/  |
+----------+------------------------------------------------------------+
    ]]></help>
    <citations>
        <citation type="bibtex">
            @PYMUONSUITE_CITATION@
        </citation>
        <citation type="doi">10.1063/1.5143190</citation>
    </citations>
</tool>