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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
author muon-spectroscopy-computational-project
date Fri, 03 Feb 2023 15:38:50 +0000
parents a2583fac03ab
children e5f1ac42b063
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1:a2583fac03ab 2:60ad7a4f1faf
1 <tool id="cif2cell" name="cif2cell" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.01"> 1 <tool id="cif2cell" name="cif2cell" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
2 <description>convert .cif file to .cell</description> 2 <description>convert .cif file to .cell</description>
3 <macros> 3 <macros>
4 <!-- version of underlying tool (PEP 440) --> 4 <!-- version of underlying tool (PEP 440) -->
5 <token name="@TOOL_VERSION@">2.0.0a3</token> 5 <token name="@TOOL_VERSION@">2.0.0a3</token>
6 <!-- version of this tool wrapper (integer) --> 6 <!-- version of this tool wrapper (integer) -->
7 <token name="@WRAPPER_VERSION@">0</token> 7 <token name="@WRAPPER_VERSION@">1</token>
8 </macros> 8 </macros>
9 <creator> 9 <creator>
10 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> 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"/> 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"/> 12 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
13 </creator> 13 </creator>
14 <requirements> 14 <requirements>
15 <requirement type="package" version="2.0.0a3">cif2cell</requirement> 15 <requirement type="package" version="2.0.0a3">cif2cell</requirement>
16 </requirements> 16 </requirements>
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 cif_structure_name=\$(sed 's/ //g' <<< "$cif_structure.name") && 18 file_name=\$(sed 's/ //g' <<< '$file.name') &&
19 ln -s $cif_structure \$cif_structure_name && 19 ln -s '$file' \$file_name &&
20 cif2cell -f \$cif_structure_name -p castep -o out.cell 20 cif2cell -f \$file_name -p castep -o out.cell
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param type="data" name="cif_structure" format="cif" label="Structure file to Convert (.cif)" /> 23 <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" />
24 </inputs> 24 </inputs>
25 <outputs> 25 <outputs>
26 <data label="Conversion of $cif_structure.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" /> 26 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" />
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test expect_num_outputs="1"> 29 <test expect_num_outputs="1">
30 <param name="cif_structure" value="Si.cif" ftype="cif" /> 30 <param name="file" value="Si.cif" ftype="cif" />
31 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" /> 31 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" />
32 </test> 32 </test>
33 <test expect_num_outputs="1"> 33 <test expect_num_outputs="1">
34 <param name="cif_structure" value="diamond.cif" ftype="cif" /> 34 <param name="file" value="diamond.cif" ftype="cif" />
35 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" /> 35 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" />
36 </test> 36 </test>
37 </tests> 37 </tests>
38 <help><![CDATA[ 38 <help><![CDATA[
39 usage: cif2cell -f file.cif -p castep -o file.cell 39 usage: cif2cell -f file.cif -p castep -o file.cell
40 40
41 Given an input .cif structure file, convert to equivalent .cell structure file. 41 Given an input .cif structure file, convert to equivalent .cell structure file.
42 Uses electronic structure program 'castep' 42 Uses electronic structure program 'castep'
43
44 cif2cell is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
43 ]]></help> 45 ]]></help>
44 <citations> 46 <citations>
45 <citation type="bibtex"> 47 <citation type="doi">10.1016/j.cpc.2011.01.013</citation>
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> 48 </citations>
62 </tool> 49 </tool>