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comparison ob_depiction_svg.xml @ 7:672b3365ddbc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:35:51 -0400
parents 88f229c63734
children d3b48303045b
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6:ed50b83b02e9 7:672b3365ddbc
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <expand macro="infile_all_types"/> 30 <expand macro="infile_all_types"/>
31 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> 31 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
32 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> 32 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="Draw all carbon atoms"/>
33 <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/> 33 <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="Use thicker lines"/>
34 34
35 <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule"> 35 <param name='display_name' type='select' format='text' label="Property to display under the molecule">
36 <option value='title'>Molecule's title</option> 36 <option value='title'>Molecule title</option>
37 <option value='MW'>Molecular Weight</option> 37 <option value='MW'>Molecular weight</option>
38 <option value='abonds'>Number of aromatic bonds</option> 38 <option value='abonds'>Number of aromatic bonds</option>
39 <option value='atoms'>Number of atoms</option> 39 <option value='atoms'>Number of atoms</option>
40 <option value='bonds'>Number of bonds</option> 40 <option value='bonds'>Number of bonds</option>
41 <option value='cansmi'>Canonical SMILES</option> 41 <option value='cansmi'>Canonical SMILES</option>
42 <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option> 42 <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option>
43 <option value='dbonds'>Number of double bonds</option> 43 <option value='dbonds'>Number of double bonds</option>
44 <option value='formula'>Chemical formula</option> 44 <option value='formula'>Chemical formula</option>
45 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> 45 <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option>
46 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> 46 <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option>
47 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
48 <option value='InChI'>IUPAC InChI identifier</option> 47 <option value='InChI'>IUPAC InChI identifier</option>
49 <option value='L5'>Lipinski Rule of Five</option> 48 <option value='L5'>Lipinski Rule of Five</option>
50 <option value='logP'>octanol/water partition coefficient</option> 49 <option value='logP'>Octanol/water partition coefficient</option>
51 <option value='MR'>molar refractivity</option> 50 <option value='MR'>Molar refractivity</option>
52 <option value='nF'>Number of Fluorine Atoms</option> 51 <option value='nF'>Number of fluorine atoms</option>
53 <option value='s'>SMARTS filter</option> 52 <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>
59 58
60 <param name='sort' type='select' format='text' optional="True" label="Sorting the displayed molecules by"> 59 <param name='sort' type='select' format='text' optional="True" label="Sort the displayed molecules (if input contains more than one) by">
61 <option value='MW'>Molecular Weight</option> 60 <option value='MW'>Molecular weight</option>
62 <option value='abonds'>Number of aromatic bonds</option> 61 <option value='abonds'>Number of aromatic bonds</option>
63 <option value='atoms'>Number of atoms</option> 62 <option value='atoms'>Number of atoms</option>
64 <option value='bonds'>Number of bonds</option> 63 <option value='bonds'>Number of bonds</option>
65 <option value='dbonds'>Number of double bonds</option> 64 <option value='dbonds'>Number of double bonds</option>
66 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> 65 <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option>
67 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> 66 <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option>
68 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
69 <option value='L5'>Lipinski Rule of Five</option> 67 <option value='L5'>Lipinski Rule of Five</option>
70 <option value='logP'>octanol/water partition coefficient</option> 68 <option value='logP'>Octanol/water partition coefficient</option>
71 <option value='MR'>molar refractivity</option> 69 <option value='MR'>Molar refractivity</option>
72 <option value='nF'>Number of Fluorine Atoms</option> 70 <option value='nF'>Number of fluorine atoms</option>
73 <option value='sbonds'>Number of single bonds</option> 71 <option value='sbonds'>Number of single bonds</option>
74 <option value='tbonds'>Number of triple bonds</option> 72 <option value='tbonds'>Number of triple bonds</option>
75 <option value='TPSA'>topological polar surface area</option> 73 <option value='TPSA'>Topological polar surface area</option>
76 </param> 74 </param>
77 75
78 <param name='oformat' type='select' format='text' label="Format of the resulting picture"> 76 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
79 <option value='svg'>SVG</option> 77 <option value='svg'>SVG</option>
80 <option value='png'>PNG</option> 78 <option value='png'>PNG</option>
103 101
104 .. class:: infomark 102 .. class:: infomark
105 103
106 **What this tool does** 104 **What this tool does**
107 105
108 Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction. 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.
109 107
110 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html 108 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
111 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html 109 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
112 110
113 ----- 111 -----