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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:02:03 +0000
parents d3b48303045b
children
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14:7672039a0bb0 15:75ee9c410951
1 <tool id="openbabel_svg_depiction" name="Visualisation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="openbabel_svg_depiction" name="Visualisation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>of compounds</description> 2 <description>of compounds</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive">
9 <![CDATA[ 9 <![CDATA[
10 obabel 10 obabel
48 <option value='InChI'>IUPAC InChI identifier</option> 48 <option value='InChI'>IUPAC InChI identifier</option>
49 <option value='L5'>Lipinski Rule of Five</option> 49 <option value='L5'>Lipinski Rule of Five</option>
50 <option value='logP'>Octanol/water partition coefficient</option> 50 <option value='logP'>Octanol/water partition coefficient</option>
51 <option value='MR'>Molar refractivity</option> 51 <option value='MR'>Molar refractivity</option>
52 <option value='nF'>Number of fluorine atoms</option> 52 <option value='nF'>Number of fluorine atoms</option>
53 <option value='s'>SMARTS filter</option>
54 <option value='sbonds'>Number of single bonds</option> 53 <option value='sbonds'>Number of single bonds</option>
55 <option value='smarts'>SMARTS filter</option> 54 <option value='smarts'>SMARTS filter</option>
56 <option value='tbonds'>Number of triple bonds</option> 55 <option value='tbonds'>Number of triple bonds</option>
57 <option value='TPSA'>topological polar surface area</option> 56 <option value='TPSA'>topological polar surface area</option>
58 </param> 57 </param>
104 103
105 **What this tool does** 104 **What this tool does**
106 105
107 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. 106 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.
108 107
109 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html 108 .. _PNG: https://open-babel.readthedocs.io/en/latest/FileFormats/PNG_2D_depiction.html
110 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html 109 .. _SVG: https://open-babel.readthedocs.io/en/latest/FileFormats/SVG_2D_depiction.html
111 110
112 ----- 111 -----
113 112
114 .. class:: warningmark 113 .. class:: warningmark
115 114