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annotate 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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60ad7a4f1faf planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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1 <tool id="cif2cell" name="cif2cell" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT">
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2 <description>convert .cif file to .cell</description>
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3 <macros>
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4 <!-- version of underlying tool (PEP 440) -->
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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5 <token name="@TOOL_VERSION@">2.0.0a3</token>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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6 <!-- version of this tool wrapper (integer) -->
4
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7 <token name="@WRAPPER_VERSION@">3</token>
0
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8 </macros>
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9 <creator>
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10 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/>
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11 <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
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e5f1ac42b063 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 70a4d37ecdf5d586703cfc509922311e95d3205c
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12 <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/>
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13 <person givenName="Maitrayee" familyName="Singh" url="https://github.com/MyTreeSings"/>
0
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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14 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
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15 </creator>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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16 <requirements>
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17 <requirement type="package" version="2.0.0a3">cif2cell</requirement>
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18 </requirements>
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19 <command detect_errors="exit_code"><![CDATA[
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20 file_name=\$(sed 's/ //g' <<< '$file.name') &&
60ad7a4f1faf planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
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21 ln -s '$file' \$file_name &&
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22 cif2cell -f \$file_name -p castep -o out.cell $no_reduce $vca $cartesian
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23 ]]></command>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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24 <inputs>
2
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25 <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" />
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0d13d09ff6b1 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit bb4b06ffc1264bd7cf5ffcfa855732768eea5a10
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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." />
0d13d09ff6b1 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit bb4b06ffc1264bd7cf5ffcfa855732768eea5a10
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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." />
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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." />
0
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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29 </inputs>
53df1118d404 planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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30 <outputs>
2
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31 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" />
0
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32 </outputs>
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33 <tests>
1
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34 <test expect_num_outputs="1">
2
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35 <param name="file" value="Si.cif" ftype="cif" />
0
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36 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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37 </test>
1
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38 <test expect_num_outputs="1">
2
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39 <param name="file" value="diamond.cif" ftype="cif" />
0
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40 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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41 </test>
4
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42 <test expect_num_outputs="1">
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43 <param name="file" value="Si.cif" ftype="cif" />
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44 <param name="no_reduce" value="--no-reduce" />
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45 <output name="out_cell" file="Si_no_reduce_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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46 </test>
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47 <test expect_num_outputs="1">
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48 <param name="file" value="Si.cif" ftype="cif" />
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49 <param name="vca" value="--vca" />
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50 <output name="out_cell" file="Si_vca_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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51 </test>
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52 <test expect_num_outputs="1">
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53 <param name="file" value="Si.cif" ftype="cif" />
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54 <param name="cartesian" value="--cartesian" />
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55 <output name="out_cell" file="Si_cartesian_out.cell" compare="diff" lines_diff="2" ftype="cell" />
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56 </test>
0
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57 </tests>
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58 <help><![CDATA[
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59 usage: cif2cell -f file.cif -p castep -o file.cell
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60
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61 Do not reduce to primitve cell: cif2cell -f file.cif -p castep -o file.cell --no-reduce
0
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62
4
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63 Set up an alloy using virtual crystal approximation: cif2cell -f file.cif -p castep -o file.cell --vca
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64
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65 Make the program generate any output in cartesian coordinates: cif2cell -f file.cif -p castep -o file.cell --cartesian
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66
3
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67 Given an input ``.cif`` structure file, convert to an equivalent ``.cell``
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68 structure file for use with electronic structure program CASTEP.
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69
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70 .. class:: warningmark
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71 warning
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72
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73 **WARNING**: ``.cif`` files may contain errors that prevent cif2cell from running properly.
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74 If you find that you run cif2cell and do not get a satisfactory ``.cell`` file,
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75 please consider revising the corresponding ``.cif`` file and, if necessary,
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76 obtaining an alternative ``.cif`` file from a suitable crystalline database.
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77
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78 cif2cell is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license.
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79 ]]></help>
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80 <citations>
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81 <citation type="doi">10.1016/j.cpc.2011.01.013</citation>
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82 </citations>
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83 </tool>