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comparison cif2cell.xml @ 5:348d3fb1d1f2 draft default tip

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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 389608650050596b28bc0c055de9f98c513a6f65
author muon-spectroscopy-computational-project
date Thu, 18 Jul 2024 09:06:52 +0000
parents 0d13d09ff6b1
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4:0d13d09ff6b1 5:348d3fb1d1f2
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@">3</token> 7 <token name="@WRAPPER_VERSION@">4</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"/>
21 ln -s '$file' \$file_name && 21 ln -s '$file' \$file_name &&
22 cif2cell -f \$file_name -p castep -o out.cell $no_reduce $vca $cartesian 22 cif2cell -f \$file_name -p castep -o out.cell $no_reduce $vca $cartesian
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <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." /> 26 <param argument="--no-reduce" type="boolean" truevalue="--no-reduce" falsevalue="" label="Preserve unit cell" help="If set, will not reduce to the primitive cell." />
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." /> 27 <param argument="--vca" type="boolean" truevalue="--vca" falsevalue="" label="Use Virtual Crystal Approximation" help="If set, will set up an alloy using the virtual crystal approximation (VCA). Currently only supported by the CASTEP interface." />
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." /> 28 <param argument="--cartesian" type="boolean" truevalue="--cartesian" falsevalue="" label="Use Cartesian coordinates" help="If set, the program generates outputs in cartesian coordinates." />
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" /> 31 <data name="out_cell" format="cell" from_work_dir="out.cell" />
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>
34 <test expect_num_outputs="1"> 34 <test expect_num_outputs="1">
35 <param name="file" value="Si.cif" ftype="cif" /> 35 <param name="file" value="Si.cif" ftype="cif" />
36 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" /> 36 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" />