| Next changeset 1:cba7123c2741 (2024-06-18) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xtb commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a |
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added:
macros.xml test-data/initial_mol.coord test-data/initial_mol.xyz xtb_molecular_optimization.xml |
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| diff -r 000000000000 -r d5633eaf3552 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 12 13:45:50 2023 +0000 |
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| @@ -0,0 +1,29 @@ +<macros> + <token name="@TOOL_VERSION@">6.6.1</token> + <xml name="creator"> + <creator> + <person + givenName="Wudmir" + familyName="Rojas" + url="https://github.com/wverastegui" + identifier="0000-0001-7036-9987" /> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI"/> + </creator> + </xml> + <token name="@HELP@"><![CDATA[ + XTB Molecular Optimization handles coord and XYZ input formats, as well as, several levels of optimization. + + Documentation + The xTB molecular optimization tool is based on the Semiempirical Tight Binding method GFNn-xTB implemented in the xtb (extended tight binding) + program package. Detailed documentation for the xtb program can be found in https://xtb-docs.readthedocs.io/en/latest/optimization.html. + ]]> + </token> +</macros> |
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| diff -r 000000000000 -r d5633eaf3552 test-data/initial_mol.coord --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/initial_mol.coord Thu Oct 12 13:45:50 2023 +0000 |
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| @@ -0,0 +1,26 @@ +$coord + -5.99455141918216 -0.78682526666358 0.39370554088116 o + -3.63830860571141 0.01577921314370 -0.52394546541572 c + -6.35936304761218 -2.10863199931285 2.70896019470081 c + -3.55829760157918 1.30103864253559 -2.83710252323663 c + -1.37182778317785 -0.42798517278855 0.80154623317728 c + -5.79337117591535 1.74470854216158 -4.15870138601214 o + -1.24576415337952 2.14009593929399 -3.80929102550083 c + 0.95939505639800 0.38378447872495 -0.17733189956940 c + 0.99635809940287 1.69597250539800 -2.49145271771405 c + 3.28572350531010 -0.11846693077585 1.30693458804557 c + 5.61705972845345 -0.10469082732464 0.32679033879514 c + 7.86643852955582 -0.65707667092152 1.94484943605965 c + -5.32333959684569 -3.93320036751666 2.66940822690469 h + -5.70103915744816 -0.93681282920432 4.32059422314034 h + -8.40293177644150 -2.50316901968901 2.95745918013747 h + -1.40671212744523 -1.41886306642894 2.59009642143871 h + -5.80002301187533 2.67033419270594 -5.83513412327771 h + -1.18548188999223 3.15210097101181 -5.58646506248980 h + 2.73579430567572 2.42368713887178 -3.27655833360389 h + 3.06831051462959 -0.59798493499297 3.28804786844385 h + 5.93406128592112 0.25488625973914 -1.65921733226687 h + 8.01034117397408 0.76605717654990 3.48047867975194 h + 9.61237539369864 -0.57937113266178 0.78425523913359 h + 7.69517265084765 -2.57395816033127 2.78205480121556 h +$end |
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| diff -r 000000000000 -r d5633eaf3552 test-data/initial_mol.xyz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/initial_mol.xyz Thu Oct 12 13:45:50 2023 +0000 |
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| @@ -0,0 +1,26 @@ +24 + +O -3.17218 -0.41637 0.20834 +C -1.92531 0.00835 -0.27726 +C -3.36523 -1.11584 1.43352 +C -1.88297 0.68848 -1.50133 +C -0.72594 -0.22648 0.42416 +O -3.06572 0.92326 -2.20069 +C -0.65923 1.13249 -2.01579 +C 0.50769 0.20309 -0.09384 +C 0.52725 0.89747 -1.31842 +C 1.73873 -0.06269 0.69160 +C 2.97242 -0.05540 0.17293 +C 4.16274 -0.34771 1.02917 +H -2.81699 -2.08136 1.41259 +H -3.01686 -0.49574 2.28636 +H -4.44664 -1.32462 1.56502 +H -0.74440 -0.75083 1.37062 +H -3.06924 1.41308 -3.08782 +H -0.62733 1.66802 -2.95623 +H 1.44772 1.28256 -1.73388 +H 1.62368 -0.31644 1.73996 +H 3.14017 0.13488 -0.87802 +H 4.23889 0.40538 1.84179 +H 5.08665 -0.30659 0.41501 +H 4.07211 -1.36208 1.47220 |
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| diff -r 000000000000 -r d5633eaf3552 xtb_molecular_optimization.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xtb_molecular_optimization.xml Thu Oct 12 13:45:50 2023 +0000 |
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| @@ -0,0 +1,59 @@ +<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09"> + <description>Semiempirical quantum mechanical molecular optimization method</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">xtb</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '${coordinates}' 'mol.${coordinates.ext}' && + xtb 'mol.${coordinates.ext}' --opt '${opt_level}' && + cp 'xtbopt.${coordinates.ext}' '${output}' + ]]></command> + <inputs> + <param label="Atomic coordinates file" type="data" name="coordinates" format="xyz" help="Initial atomic coordinates file to be optimized."/> + <param type="select" label="Optimization Levels" name="opt_level" help="Geometry optimization convergence levels." > + <option value="crude">crude</option> + <option value="sloppy">sloppy</option> + <option value="loose">loose</option> + <option value="lax">lax</option> + <option value="normal">normal</option> + <option value="tight">tight</option> + <option value="vtight">vtight</option> + <option value="extreme">extreme</option> + </param> + </inputs> + <outputs> + <data name="output" format_source="coordinates" /> + </outputs> + <tests> + <test> + <param name="coordinates" value="initial_mol.xyz" ftype="xyz"/> + <output name="output"> + <assert_contents> + <has_text text="xtb"/> + <has_n_lines n="26"/> + </assert_contents> + </output> + </test> + <!-- <test> + <param name="coordinates" value="initial_mol.coord" ftype="coord"/> + <output name="output" file="optimized_mol.coord" ftype="coord"> + <assert_contents> + <has_text text="$coord"/> + <has_n_lines min="26"/> + </assert_contents> + </output> + </test> --> + </tests> + <help> + <![CDATA[ + @HELP@ + ]]> + </help> + <citations> + <citation type="doi">https://doi.org/10.1002/wcms.1493</citation> + </citations> +</tool> |