| Previous changeset 6:ed50b83b02e9 (2018-09-03) Next changeset 8:136ceea822f5 (2019-05-10) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e |
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modified:
macros.xml ob_depiction_svg.xml |
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added:
test-data/2_mol.dat test-data/CO.smarts |
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| diff -r ed50b83b02e9 -r 672b3365ddbc macros.xml --- a/macros.xml Mon Sep 03 16:41:32 2018 -0400 +++ b/macros.xml Tue May 07 13:35:51 2019 -0400 |
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| @@ -1,9 +1,10 @@ <macros> - <token name="@VERSION@">2.4.1</token> + <token name="@VERSION@">2.4.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.4.1">openbabel</requirement> + <requirement type="package" version="3">python</requirement> <yield /> </requirements> </xml> @@ -37,6 +38,3 @@ </citations> </xml> </macros> - - - |
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| diff -r ed50b83b02e9 -r 672b3365ddbc ob_depiction_svg.xml --- a/ob_depiction_svg.xml Mon Sep 03 16:41:32 2018 -0400 +++ b/ob_depiction_svg.xml Tue May 07 13:35:51 2019 -0400 |
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| @@ -29,12 +29,12 @@ <inputs> <expand macro="infile_all_types"/> <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> - <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> - <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/> + <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="Draw all carbon atoms"/> + <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="Use thicker lines"/> - <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule"> - <option value='title'>Molecule's title</option> - <option value='MW'>Molecular Weight</option> + <param name='display_name' type='select' format='text' label="Property to display under the molecule"> + <option value='title'>Molecule title</option> + <option value='MW'>Molecular weight</option> <option value='abonds'>Number of aromatic bonds</option> <option value='atoms'>Number of atoms</option> <option value='bonds'>Number of bonds</option> @@ -42,14 +42,13 @@ <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option> <option value='dbonds'>Number of double bonds</option> <option value='formula'>Chemical formula</option> - <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> - <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> - <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option> + <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option> + <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option> <option value='InChI'>IUPAC InChI identifier</option> <option value='L5'>Lipinski Rule of Five</option> - <option value='logP'>octanol/water partition coefficient</option> - <option value='MR'>molar refractivity</option> - <option value='nF'>Number of Fluorine Atoms</option> + <option value='logP'>Octanol/water partition coefficient</option> + <option value='MR'>Molar refractivity</option> + <option value='nF'>Number of fluorine atoms</option> <option value='s'>SMARTS filter</option> <option value='sbonds'>Number of single bonds</option> <option value='smarts'>SMARTS filter</option> @@ -57,22 +56,21 @@ <option value='TPSA'>topological polar surface area</option> </param> - <param name='sort' type='select' format='text' optional="True" label="Sorting the displayed molecules by"> - <option value='MW'>Molecular Weight</option> + <param name='sort' type='select' format='text' optional="True" label="Sort the displayed molecules (if input contains more than one) by"> + <option value='MW'>Molecular weight</option> <option value='abonds'>Number of aromatic bonds</option> <option value='atoms'>Number of atoms</option> <option value='bonds'>Number of bonds</option> <option value='dbonds'>Number of double bonds</option> - <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> - <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> - <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option> + <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option> + <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option> <option value='L5'>Lipinski Rule of Five</option> - <option value='logP'>octanol/water partition coefficient</option> - <option value='MR'>molar refractivity</option> - <option value='nF'>Number of Fluorine Atoms</option> + <option value='logP'>Octanol/water partition coefficient</option> + <option value='MR'>Molar refractivity</option> + <option value='nF'>Number of fluorine atoms</option> <option value='sbonds'>Number of single bonds</option> <option value='tbonds'>Number of triple bonds</option> - <option value='TPSA'>topological polar surface area</option> + <option value='TPSA'>Topological polar surface area</option> </param> <param name='oformat' type='select' format='text' label="Format of the resulting picture"> @@ -105,7 +103,7 @@ **What this tool does** -Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction. +Creates an SVG or PNG image of a small set of molecules (not more than a few hundred). Based on Open Babel PNG_/SVG_ 2D depiction. Note that PNG is a poor choice for representing more than one molecule, as resolution will be low. .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html |
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| diff -r ed50b83b02e9 -r 672b3365ddbc test-data/2_mol.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mol.dat Tue May 07 13:35:51 2019 -0400 |
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| @@ -0,0 +1,2 @@ +CC(=O)OC1=CC=CC=C1C(=O)[O-] +CC(=O)OC1=CC=CC=C1C(=O)[O-] |
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| diff -r ed50b83b02e9 -r 672b3365ddbc test-data/CO.smarts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CO.smarts Tue May 07 13:35:51 2019 -0400 |
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| @@ -0,0 +1,1 @@ +CO |