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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:45:50 +0000
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d5633eaf3552 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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1 <tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09">
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2 <description>Semiempirical quantum mechanical molecular optimization method</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">xtb</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
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12 xtb 'mol.${coordinates.ext}' --opt '${opt_level}' &&
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13 cp 'xtbopt.${coordinates.ext}' '${output}'
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14 ]]></command>
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15 <inputs>
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16 <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
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17 <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." >
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18 <option value="crude">crude</option>
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19 <option value="sloppy">sloppy</option>
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20 <option value="loose">loose</option>
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21 <option value="lax">lax</option>
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22 <option value="normal">normal</option>
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23 <option value="tight">tight</option>
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24 <option value="vtight">vtight</option>
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25 <option value="extreme">extreme</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data name="output" format_source="coordinates" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="coordinates" value="initial_mol.xyz" ftype="xyz"/>
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34 <output name="output">
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35 <assert_contents>
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36 <has_text text="xtb"/>
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37 <has_n_lines n="26"/>
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38 </assert_contents>
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39 </output>
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40 </test>
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41 <!-- <test>
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42 <param name="coordinates" value="initial_mol.coord" ftype="coord"/>
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43 <output name="output" file="optimized_mol.coord" ftype="coord">
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44 <assert_contents>
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45 <has_text text="$coord"/>
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46 <has_n_lines min="26"/>
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47 </assert_contents>
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48 </output>
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49 </test> -->
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50 </tests>
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51 <help>
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52 <![CDATA[
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53 @HELP@
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54 ]]>
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55 </help>
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56 <citations>
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57 <citation type="doi">https://doi.org/10.1002/wcms.1493</citation>
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58 </citations>
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59 </tool>