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author muon-spectroscopy-computational-project
date Thu, 15 Sep 2022 10:23:01 +0000
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1 <tool id="cif2cell" name="cif2cell" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01">
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2 <description>convert .cif file to .cell</description>
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3 <macros>
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4 <!-- version of underlying tool (PEP 440) -->
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5 <token name="@TOOL_VERSION@">2.0.0a3</token>
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6 <!-- version of this tool wrapper (integer) -->
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7 <token name="@WRAPPER_VERSION@">0</token>
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8 </macros>
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9 <creator>
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10 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
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11 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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12 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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13 </creator>
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14 <requirements>
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15 <requirement type="package" version="2.0.0a3">cif2cell</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
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18 cif_structure_name=\$(sed 's/ //g' <<< "$cif_structure.name") &&
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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19 ln -s $cif_structure \$cif_structure_name &&
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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20 cif2cell -f \$cif_structure_name -p castep -o out.cell
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21 ]]></command>
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22 <inputs>
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23 <param type="data" name="cif_structure" format="cif" label="Structure file to Convert (.cif)" />
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24 </inputs>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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25 <outputs>
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26 <data label="Conversion of $cif_structure.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" />
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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27 </outputs>
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28 <tests>
1
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29 <test expect_num_outputs="1">
0
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30 <param name="cif_structure" value="Si.cif" ftype="cif" />
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31 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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32 </test>
1
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33 <test expect_num_outputs="1">
0
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34 <param name="cif_structure" value="diamond.cif" ftype="cif" />
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35 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 usage: cif2cell -f file.cif -p castep -o file.cell
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40
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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41 Given an input .cif structure file, convert to equivalent .cell structure file.
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42 Uses electronic structure program 'castep'
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43 ]]></help>
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44 <citations>
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45 <citation type="bibtex">
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46 @article{cif2cell,
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47 author = {Torbj\"orn Bj\"orkman},
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48 title = {CIF2Cell: Generating geometries for electronic structure programs},
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49 journal = {Computer Physics Communications},
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50 volume = {182},
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51 number = {5},
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52 pages = {1183 - 1186},
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53 year = {2011},
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54 issn = {0010-4655},
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55 doi={10.1016/j.cpc.2011.01.013},
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56 URL={
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57 http://www.sciencedirect.com/science/article/pii/S0010465511000336
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58 }
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59 }
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60 </citation>
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61 </citations>
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62 </tool>