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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit 68505a19637f8374cc5bde7e6b9370647a064ca9
author recetox
date Thu, 25 Jul 2024 14:27:18 +0000
parents cba7123c2741
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6e1ef071fffc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit 68505a19637f8374cc5bde7e6b9370647a064ca9
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1 <tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy3" profile="21.09">
0
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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>
2
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6 <expand macro="edam"/>
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7 <expand macro="creator"/>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">xtb</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
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13 xtb 'mol.${coordinates.ext}' --opt '${opt_level}' &&
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15 #if $replace_second_line == "FALSE":
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16 cp 'xtbopt.${coordinates.ext}' '${output}'
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17 #end if
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19 #if $replace_second_line == "TRUE":
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20 cp 'xtbopt.${coordinates.ext}' '${output}' &&
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21 awk 'NR==FNR{if(NR==2) line=$0; next} {if(FNR==2) print line; else print $0}' '${coordinates}' '${output}' > final &&
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22 mv final '${output}'
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23 #end if
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25
0
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26 ]]></command>
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27 <inputs>
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28 <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
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29 <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." >
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30 <option value="crude">crude</option>
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31 <option value="sloppy">sloppy</option>
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32 <option value="loose">loose</option>
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33 <option value="lax">lax</option>
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34 <option value="normal">normal</option>
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35 <option value="tight">tight</option>
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36 <option value="vtight">vtight</option>
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37 <option value="extreme">extreme</option>
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38 </param>
1
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39 <param type="boolean" name="replace_second_line" label = "Keep molecule name" truevalue="TRUE" falsevalue="FALSE" checked="false" help = "If YES, the molecule name from the coordinates file is preserved, if it exists. Otherwise, the energy, gnorm, and xtb version are printed." />
0
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40 </inputs>
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41 <outputs>
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42 <data name="output" format_source="coordinates" />
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43 </outputs>
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44 <tests>
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45 <test>
1
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46 <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
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47 <param name="replace_second_line" value="TRUE" />
0
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48 <output name="output">
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49 <assert_contents>
1
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50 <has_text text="Benzophenone"/>
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51 </assert_contents>
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52 </output>
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53 </test>
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54 <test>
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55 <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
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56 <param name="replace_second_line" value="FALSE" />
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57 <output name="output">
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58 <assert_contents>
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59 <has_text text="energy"/>
0
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60 </assert_contents>
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61 </output>
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62 </test>
1
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63 <test>
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64 <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
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65 <param name="replace_second_line" value="TRUE" />
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66 <output name="output">
0
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67 <assert_contents>
1
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68 <not_has_text text="energy"/>
0
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69 </assert_contents>
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70 </output>
1
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71 </test>
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72 <test>
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73 <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
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74 <param name="replace_second_line" value="FALSE" />
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75 <output name="output">
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76 <assert_contents>
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77 <has_text text="energy"/>
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78 </assert_contents>
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79 </output>
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80 </test>
0
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81 </tests>
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82 <help>
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83 <![CDATA[
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84 @HELP@
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85 ]]>
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86 </help>
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87 <citations>
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88 <citation type="doi">https://doi.org/10.1002/wcms.1493</citation>
d5633eaf3552 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents:
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89 </citations>
d5633eaf3552 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents:
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90 </tool>