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author muon-spectroscopy-computational-project
date Tue, 18 Jul 2023 13:27:02 +0000
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c062cefbb20f planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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1 <tool id="pm_symmetry" name="PyMuonSuite Symmetry" version="@PYMUONSUITE_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>generate Wyckoff points symmetry report</description>
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3 <macros>
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4 <!-- version of this tool wrapper (integer) -->
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5 <token name="@WRAPPER_VERSION@">0</token>
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6 <import>muon_macros.xml</import>
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7 </macros>
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8 <creator>
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9 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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10 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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11 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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12 </creator>
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13 <requirements>
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14 <requirement type="package" version="@PYMUONSUITE_VERSION@">pymuonsuite</requirement>
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15 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 structure_name_internal=\$(sed 's/ /\_/g' <<< '$structure.name') &&
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18 ln -s '$structure' \$structure_name_internal &&
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19 pm-symmetry \$structure_name_internal > out.txt
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="structure" label="Structure file" format="cell,cif,xyz,extxyz" help="The structure to calculate symmetries of. Accepted file types: cell."/>
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23 </inputs>
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24 <outputs>
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25 <data label="symmetry of $structure.name" name="symmetry_report" format="txt" from_work_dir="out.txt"/>
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26 </outputs>
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27 <tests>
1
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28 <test expect_num_outputs="1">
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29 <param name="structure" value="Si.cell" ftype="cell"/>
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30 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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31 </test>
1
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32 <test expect_num_outputs="1">
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33 <param name="structure" value="Si.cif" ftype="cif"/>
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34 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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35 </test>
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36 <test expect_failure="true">
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37 <param name="structure" value="Si.xyz" ftype="xyz"/>
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38 <assert_stderr>
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39 <has_text text="TypeError: 'NoneType' object is not subscriptable"/>
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40 </assert_stderr>
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41 </test>
1
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42 <test expect_num_outputs="1">
0
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43 <param name="structure" value="Si.extxyz" ftype="extxyz"/>
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44 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 usage: pm-symmetry structure
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49
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50 Given an input structure, generates a Wyckoff points symmetry report for that structure.
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51
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52 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
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53 ]]></help>
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54 <citations>
3
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55 <citation type="doi">@PYMUONSUITE_CITATION@</citation>
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56 <citation type="doi">10.1063/5.0012381</citation>
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57 </citations>
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58 </tool>