Mercurial > repos > muon-spectroscopy-computational-project > cif2cell
annotate cif2cell.xml @ 2:60ad7a4f1faf draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
| author | muon-spectroscopy-computational-project |
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| date | Fri, 03 Feb 2023 15:38:50 +0000 |
| parents | a2583fac03ab |
| children | e5f1ac42b063 |
| rev | line source |
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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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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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2 <description>convert .cif file to .cell</description> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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3 <macros> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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4 <!-- version of underlying tool (PEP 440) --> |
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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> |
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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) --> |
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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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7 <token name="@WRAPPER_VERSION@">1</token> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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8 </macros> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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9 <creator> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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10 <person givenName="Anish" familyName="Mudaraddi" identifier="https://orcid.org/0000-0002-2135-2705"/> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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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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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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12 <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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13 </creator> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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14 <requirements> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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15 <requirement type="package" version="2.0.0a3">cif2cell</requirement> |
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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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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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17 <command detect_errors="exit_code"><![CDATA[ |
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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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18 file_name=\$(sed 's/ //g' <<< '$file.name') && |
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60ad7a4f1faf
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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19 ln -s '$file' \$file_name && |
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60ad7a4f1faf
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
muon-spectroscopy-computational-project
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20 cif2cell -f \$file_name -p castep -o out.cell |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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21 ]]></command> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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22 <inputs> |
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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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23 <param type="data" argument="--file" format="cif" label="Structure file to Convert (.cif)" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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24 </inputs> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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25 <outputs> |
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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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26 <data label="Conversion of $file.name to .cell" name="out_cell" format="cell" from_work_dir="out.cell" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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27 </outputs> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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28 <tests> |
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a2583fac03ab
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb
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29 <test expect_num_outputs="1"> |
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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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30 <param name="file" value="Si.cif" ftype="cif" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
muon-spectroscopy-computational-project
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31 <output name="out_cell" file="Si_out.cell" compare="diff" lines_diff="2" ftype="cell" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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32 </test> |
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a2583fac03ab
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit 6a07c4caed5ef35f35198d54ebafd7d1d6d60edb
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33 <test expect_num_outputs="1"> |
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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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34 <param name="file" value="diamond.cif" ftype="cif" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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35 <output name="out_cell" file="diamond_out.cell" compare="diff" lines_diff="2" ftype="cell" /> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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36 </test> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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37 </tests> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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38 <help><![CDATA[ |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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39 usage: cif2cell -f file.cif -p castep -o file.cell |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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40 |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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41 Given an input .cif structure file, convert to equivalent .cell structure file. |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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42 Uses electronic structure program 'castep' |
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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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43 |
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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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44 cif2cell is distributed under the GPLv3 license. This tool wrapper is distributed under the MIT license. |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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45 ]]></help> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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46 <citations> |
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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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47 <citation type="doi">10.1016/j.cpc.2011.01.013</citation> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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48 </citations> |
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53df1118d404
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/cif2cell commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
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49 </tool> |