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comparison cif2cell.xml @ 4:0d13d09ff6b1 draft

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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit bb4b06ffc1264bd7cf5ffcfa855732768eea5a10
author muon-spectroscopy-computational-project
date Fri, 01 Dec 2023 11:17:36 +0000
parents e5f1ac42b063
children 348d3fb1d1f2
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3:e5f1ac42b063 4:0d13d09ff6b1
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@">2</token> 7 <token name="@WRAPPER_VERSION@">3</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 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> 12 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
13 <person givenName="Maitrayee" familyName="Singh" url="https://github.com/MyTreeSings"/>
13 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> 14 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
14 </creator> 15 </creator>
15 <requirements> 16 <requirements>
16 <requirement type="package" version="2.0.0a3">cif2cell</requirement> 17 <requirement type="package" version="2.0.0a3">cif2cell</requirement>
17 </requirements> 18 </requirements>
18 <command detect_errors="exit_code"><![CDATA[ 19 <command detect_errors="exit_code"><![CDATA[
19 file_name=\$(sed 's/ //g' <<< '$file.name') && 20 file_name=\$(sed 's/ //g' <<< '$file.name') &&
20 ln -s '$file' \$file_name && 21 ln -s '$file' \$file_name &&
21 cif2cell -f \$file_name -p castep -o out.cell 22 cif2cell -f \$file_name -p castep -o out.cell $no_reduce $vca $cartesian
22 ]]></command> 23 ]]></command>
23 <inputs> 24 <inputs>
24 <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" /> 25 <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" />
26 <param argument="--no-reduce" type="boolean" truevalue="--no-reduce" falsevalue="" label="Do you want to construct a primitive cell using --no-reduce?" help="Use a cif file to convert into a structural (cell) file." />
27 <param argument="--vca" type="boolean" truevalue="--vca" falsevalue="" label="Do you want to set up an alloy using Virtual Crystal Approximation?" help="Use a cif file to convert into a structural (cell) file." />
28 <param argument="--cartesian" type="boolean" truevalue="--cartesian" falsevalue="" label="Do you want to generate any output in cartesian coordinates?" help="Use a cif file to convert into a structural (cell) file." />
25 </inputs> 29 </inputs>
26 <outputs> 30 <outputs>
27 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" /> 31 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" />
28 </outputs> 32 </outputs>
29 <tests> 33 <tests>
33 </test> 37 </test>
34 <test expect_num_outputs="1"> 38 <test expect_num_outputs="1">
35 <param name="file" value="diamond.cif" ftype="cif" /> 39 <param name="file" value="diamond.cif" ftype="cif" />
36 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" /> 40 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" />
37 </test> 41 </test>
42 <test expect_num_outputs="1">
43 <param name="file" value="Si.cif" ftype="cif" />
44 <param name="no_reduce" value="--no-reduce" />
45 <output name="out_cell" file="Si_no_reduce_out.cell" compare="diff" lines_diff="2" ftype="cell" />
46 </test>
47 <test expect_num_outputs="1">
48 <param name="file" value="Si.cif" ftype="cif" />
49 <param name="vca" value="--vca" />
50 <output name="out_cell" file="Si_vca_out.cell" compare="diff" lines_diff="2" ftype="cell" />
51 </test>
52 <test expect_num_outputs="1">
53 <param name="file" value="Si.cif" ftype="cif" />
54 <param name="cartesian" value="--cartesian" />
55 <output name="out_cell" file="Si_cartesian_out.cell" compare="diff" lines_diff="2" ftype="cell" />
56 </test>
38 </tests> 57 </tests>
39 <help><![CDATA[ 58 <help><![CDATA[
40 usage: cif2cell -f file.cif -p castep -o file.cell 59 usage: cif2cell -f file.cif -p castep -o file.cell
60
61 Do not reduce to primitve cell: cif2cell -f file.cif -p castep -o file.cell --no-reduce
41 62
63 Set up an alloy using virtual crystal approximation: cif2cell -f file.cif -p castep -o file.cell --vca
64
65 Make the program generate any output in cartesian coordinates: cif2cell -f file.cif -p castep -o file.cell --cartesian
66
42 Given an input ``.cif`` structure file, convert to an equivalent ``.cell`` 67 Given an input ``.cif`` structure file, convert to an equivalent ``.cell``
43 structure file for use with electronic structure program CASTEP. 68 structure file for use with electronic structure program CASTEP.
44 69
45 .. class:: warningmark 70 .. class:: warningmark
46 warning 71 warning