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comparison xtb_molecular_optimization.xml @ 0:d5633eaf3552 draft

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