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