Mercurial > repos > muon-spectroscopy-computational-project > pm_symmetry
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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author | muon-spectroscopy-computational-project |
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date | Fri, 03 Feb 2023 15:40:00 +0000 |
parents | d8146a73b011 |
children | c062cefbb20f |
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<tool id="pm_symmetry" name="PyMuonSuite Symmetry" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> <description>generate Wyckoff points symmetry report</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="@TOOL_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> <requirement type="package" version="@TOOL_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 label="symmetry of $structure.name" 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="bibtex"> @TOOL_CITATION@ </citation> <citation type="doi">10.1063/5.0012381</citation> </citations> </tool>