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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
date Fri, 03 Feb 2023 15:40:00 +0000
parents d8146a73b011
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620ab6826b9b planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="pm_symmetry" name="PyMuonSuite Symmetry" version="@TOOL_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 underlying tool (PEP 440) -->
2
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5 <token name="@TOOL_VERSION@">0.2.3</token>
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6 <!-- version of this tool wrapper (integer) -->
2
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7 <token name="@WRAPPER_VERSION@">0</token>
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8 <!-- citation should be updated with every underlying tool version -->
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9 <!-- typical fields to update are version, month, year, and doi -->
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10 <token name="@TOOL_CITATION@">
2
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11 @software{Sturniolo_pymuon-suite_2022,
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12 author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
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13 license = {GPL-3.0},
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14 month = {8},
0
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15 title = {{pymuon-suite}},
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16 url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
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17 version = {v0.2.3},
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18 doi = {10.5281/zenodo.7025644},
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19 year = {2022}
0
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20 }
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21 </token>
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22 </macros>
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23 <creator>
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24 <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
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25 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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26 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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27 </creator>
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28 <requirements>
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29 <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement>
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30 </requirements>
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31 <command detect_errors="exit_code"><![CDATA[
2
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32 structure_name_internal=\$(sed 's/ /\_/g' <<< '$structure.name') &&
620ab6826b9b planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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33 ln -s '$structure' \$structure_name_internal &&
0
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34 pm-symmetry \$structure_name_internal > out.txt
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35 ]]></command>
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36 <inputs>
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37 <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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38 </inputs>
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39 <outputs>
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40 <data label="symmetry of $structure.name" name="symmetry_report" format="txt" from_work_dir="out.txt"/>
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41 </outputs>
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42 <tests>
1
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43 <test expect_num_outputs="1">
0
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44 <param name="structure" value="Si.cell" ftype="cell"/>
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45 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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46 </test>
1
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47 <test expect_num_outputs="1">
0
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48 <param name="structure" value="Si.cif" ftype="cif"/>
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49 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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50 </test>
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51 <test expect_failure="true">
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52 <param name="structure" value="Si.xyz" ftype="xyz"/>
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53 <assert_stderr>
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54 <has_text text="TypeError: 'NoneType' object is not subscriptable"/>
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55 </assert_stderr>
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56 </test>
1
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57 <test expect_num_outputs="1">
0
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58 <param name="structure" value="Si.extxyz" ftype="extxyz"/>
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59 <output name="symmetry_report" file="test_out.txt" ftype="txt" compare="re_match_multiline"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 usage: pm-symmetry structure
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64
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65 Given an input structure, generates a Wyckoff points symmetry report for that structure.
2
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66
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67 PyMuonSuite is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
0
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68 ]]></help>
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69 <citations>
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70 <citation type="bibtex">
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71 @TOOL_CITATION@
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72 </citation>
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73 <citation type="doi">10.1063/5.0012381</citation>
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74 </citations>
39d7644724dc planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_symmetry commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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75 </tool>