annotate pm_symmetry.xml @ 4:34c550d15bd4 draft default tip

planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit 389608650050596b28bc0c055de9f98c513a6f65

<tool id="pm_symmetry" name="PyMuonSuite Symmetry" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
    <description>generate Wyckoff points symmetry report</description>
    <macros>
        <!-- version of this tool wrapper (integer) -->
        <token name="@WRAPPER_VERSION@">1</token>
        <import>muon_macros.xml</import>
    </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>
        <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        structure_name_internal=\$(sed 's/ /\_/g' <<< '$structure.name') &&
        ln -s '$structure' \$structure_name_internal &&
        pm-symmetry \$structure_name_internal > out.txt
    ]]></command>
    <inputs>
        <param type="data" name="structure" label="Structure file" format="cell,cif,xyz,extxyz" help="The structure to calculate symmetries of. Accepted file types: cell."/>
    </inputs>
    <outputs>
        <data name="symmetry_report" format="txt" from_work_dir="out.txt"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="structure" value="Si.cell" ftype="cell"/>
            <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
        </test>
        <test expect_num_outputs="1">
            <param name="structure" value="Si.cif" ftype="cif"/>
            <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
        </test>
        <test expect_failure="true">
            <param name="structure" value="Si.xyz" ftype="xyz"/>
            <assert_stderr>
                <has_text text="TypeError: 'NoneType' object is not subscriptable"/>
            </assert_stderr>
        </test>
        <test expect_num_outputs="1">
            <param name="structure" value="Si.extxyz" ftype="extxyz"/>
            <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
        </test>
    </tests>
    <help><![CDATA[
        usage: pm-symmetry structure

        Given an input structure, generates a Wyckoff points symmetry report for that structure.
        
        PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
    ]]></help>
    <citations>
        <citation type="doi">@PYMUONSUITE_CITATION@</citation>
        <citation type="doi">10.1063/5.0012381</citation>
    </citations>
</tool>