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comparison xtb_molecular_optimization.xml @ 1:cba7123c2741 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit 070a3fd9e44e71efcf7a4490d91d1cee5a4711ce
author recetox
date Tue, 18 Jun 2024 07:53:15 +0000
parents d5633eaf3552
children 6e1ef071fffc
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0:d5633eaf3552 1:cba7123c2741
1 <tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09"> 1 <tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy2" profile="21.09">
2 <description>Semiempirical quantum mechanical molecular optimization method</description> 2 <description>Semiempirical quantum mechanical molecular optimization method</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/> 6 <expand macro="creator"/>
8 <requirement type="package" version="@TOOL_VERSION@">xtb</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">xtb</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 ln -s '${coordinates}' 'mol.${coordinates.ext}' && 11 ln -s '${coordinates}' 'mol.${coordinates.ext}' &&
12 xtb 'mol.${coordinates.ext}' --opt '${opt_level}' && 12 xtb 'mol.${coordinates.ext}' --opt '${opt_level}' &&
13 cp 'xtbopt.${coordinates.ext}' '${output}' 13
14 #if $replace_second_line == "FALSE":
15 cp 'xtbopt.${coordinates.ext}' '${output}'
16 #end if
17
18 #if $replace_second_line == "TRUE":
19 cp 'xtbopt.${coordinates.ext}' '${output}' &&
20 awk 'NR==FNR{if(NR==2) line=$0; next} {if(FNR==2) print line; else print $0}' '${coordinates}' '${output}' > final &&
21 mv final '${output}'
22 #end if
23
24
14 ]]></command> 25 ]]></command>
15 <inputs> 26 <inputs>
16 <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/> 27 <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/>
17 <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." > 28 <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." >
18 <option value="crude">crude</option> 29 <option value="crude">crude</option>
22 <option value="normal">normal</option> 33 <option value="normal">normal</option>
23 <option value="tight">tight</option> 34 <option value="tight">tight</option>
24 <option value="vtight">vtight</option> 35 <option value="vtight">vtight</option>
25 <option value="extreme">extreme</option> 36 <option value="extreme">extreme</option>
26 </param> 37 </param>
38 <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." />
27 </inputs> 39 </inputs>
28 <outputs> 40 <outputs>
29 <data name="output" format_source="coordinates" /> 41 <data name="output" format_source="coordinates" />
30 </outputs> 42 </outputs>
31 <tests> 43 <tests>
32 <test> 44 <test>
33 <param name="coordinates" value="initial_mol.xyz" ftype="xyz"/> 45 <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
46 <param name="replace_second_line" value="TRUE" />
34 <output name="output"> 47 <output name="output">
35 <assert_contents> 48 <assert_contents>
36 <has_text text="xtb"/> 49 <has_text text="Benzophenone"/>
37 <has_n_lines n="26"/>
38 </assert_contents> 50 </assert_contents>
39 </output> 51 </output>
40 </test> 52 </test>
41 <!-- <test> 53 <test>
42 <param name="coordinates" value="initial_mol.coord" ftype="coord"/> 54 <param name="coordinates" value="initial_mol_molname.xyz" ftype="xyz"/>
43 <output name="output" file="optimized_mol.coord" ftype="coord"> 55 <param name="replace_second_line" value="FALSE" />
56 <output name="output">
44 <assert_contents> 57 <assert_contents>
45 <has_text text="$coord"/> 58 <has_text text="energy"/>
46 <has_n_lines min="26"/>
47 </assert_contents> 59 </assert_contents>
48 </output> 60 </output>
49 </test> --> 61 </test>
62 <test>
63 <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
64 <param name="replace_second_line" value="TRUE" />
65 <output name="output">
66 <assert_contents>
67 <not_has_text text="energy"/>
68 </assert_contents>
69 </output>
70 </test>
71 <test>
72 <param name="coordinates" value="initial_mol_no_molname.xyz" ftype="xyz"/>
73 <param name="replace_second_line" value="FALSE" />
74 <output name="output">
75 <assert_contents>
76 <has_text text="energy"/>
77 </assert_contents>
78 </output>
79 </test>
50 </tests> 80 </tests>
51 <help> 81 <help>
52 <![CDATA[ 82 <![CDATA[
53 @HELP@ 83 @HELP@
54 ]]> 84 ]]>