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author | muon-spectroscopy-computational-project |
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date | Fri, 01 Dec 2023 11:17:36 +0000 |
parents | e5f1ac42b063 |
children | 348d3fb1d1f2 |
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<tool id="cif2cell" name="cif2cell" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> <description>convert .cif file to .cell</description> <macros> <!-- version of underlying tool (PEP 440) --> <token name="@TOOL_VERSION@">2.0.0a3</token> <!-- version of this tool wrapper (integer) --> <token name="@WRAPPER_VERSION@">3</token> </macros> <creator> <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/> <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> <person givenName="Maitrayee" familyName="Singh" url="https://github.com/MyTreeSings"/> <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> </creator> <requirements> <requirement type="package" version="2.0.0a3">cif2cell</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ file_name=\$(sed 's/ //g' <<< '$file.name') && ln -s '$file' \$file_name && cif2cell -f \$file_name -p castep -o out.cell $no_reduce $vca $cartesian ]]></command> <inputs> <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" /> <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." /> <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." /> <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." /> </inputs> <outputs> <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="file" value="Si.cif" ftype="cif" /> <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" /> </test> <test expect_num_outputs="1"> <param name="file" value="diamond.cif" ftype="cif" /> <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" /> </test> <test expect_num_outputs="1"> <param name="file" value="Si.cif" ftype="cif" /> <param name="no_reduce" value="--no-reduce" /> <output name="out_cell" file="Si_no_reduce_out.cell" compare="diff" lines_diff="2" ftype="cell" /> </test> <test expect_num_outputs="1"> <param name="file" value="Si.cif" ftype="cif" /> <param name="vca" value="--vca" /> <output name="out_cell" file="Si_vca_out.cell" compare="diff" lines_diff="2" ftype="cell" /> </test> <test expect_num_outputs="1"> <param name="file" value="Si.cif" ftype="cif" /> <param name="cartesian" value="--cartesian" /> <output name="out_cell" file="Si_cartesian_out.cell" compare="diff" lines_diff="2" ftype="cell" /> </test> </tests> <help><![CDATA[ usage: cif2cell -f file.cif -p castep -o file.cell Do not reduce to primitve cell: cif2cell -f file.cif -p castep -o file.cell --no-reduce Set up an alloy using virtual crystal approximation: cif2cell -f file.cif -p castep -o file.cell --vca Make the program generate any output in cartesian coordinates: cif2cell -f file.cif -p castep -o file.cell --cartesian Given an input ``.cif`` structure file, convert to an equivalent ``.cell`` structure file for use with electronic structure program CASTEP. .. class:: warningmark warning **WARNING**: ``.cif`` files may contain errors that prevent cif2cell from running properly. If you find that you run cif2cell and do not get a satisfactory ``.cell`` file, please consider revising the corresponding ``.cif`` file and, if necessary, obtaining an alternative ``.cif`` file from a suitable crystalline database. cif2cell is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license. ]]></help> <citations> <citation type="doi">10.1016/j.cpc.2011.01.013</citation> </citations> </tool>