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annotate ob_depiction_svg.xml @ 15:75ee9c410951 draft default tip

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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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d3b48303045b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="openbabel_svg_depiction" name="Visualisation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>of compounds</description>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive">
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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9 <![CDATA[
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10 obabel
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11 -i${infile.ext}
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 "${infile}"
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13 $embed_molecule_as_cml
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14 $draw_all_carbon_atoms
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 -xC
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16 -O
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17 "${outfile}"
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18 -o$oformat
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19 #if $sort:
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20 --sort $sort
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21 #end if
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22 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title':
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23 --append "$display_name"
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 --title ""
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25 #end if
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26 $thick_lines
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27 2>&1
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28 ]]>
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29 </command>
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30 <inputs>
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31 <expand macro="infile_all_types"/>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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32 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
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33 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="Draw all carbon atoms"/>
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34 <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="Use thicker lines"/>
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35
7
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36 <param name='display_name' type='select' format='text' label="Property to display under the molecule">
672b3365ddbc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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37 <option value='title'>Molecule title</option>
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38 <option value='MW'>Molecular weight</option>
0
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39 <option value='abonds'>Number of aromatic bonds</option>
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40 <option value='atoms'>Number of atoms</option>
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41 <option value='bonds'>Number of bonds</option>
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42 <option value='cansmi'>Canonical SMILES</option>
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43 <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option>
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44 <option value='dbonds'>Number of double bonds</option>
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45 <option value='formula'>Chemical formula</option>
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46 <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option>
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47 <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option>
0
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48 <option value='InChI'>IUPAC InChI identifier</option>
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49 <option value='L5'>Lipinski Rule of Five</option>
7
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50 <option value='logP'>Octanol/water partition coefficient</option>
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51 <option value='MR'>Molar refractivity</option>
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52 <option value='nF'>Number of fluorine atoms</option>
0
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53 <option value='sbonds'>Number of single bonds</option>
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54 <option value='smarts'>SMARTS filter</option>
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55 <option value='tbonds'>Number of triple bonds</option>
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56 <option value='TPSA'>topological polar surface area</option>
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57 </param>
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58
7
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59 <param name='sort' type='select' format='text' optional="True" label="Sort the displayed molecules (if input contains more than one) by">
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60 <option value='MW'>Molecular weight</option>
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61 <option value='abonds'>Number of aromatic bonds</option>
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62 <option value='atoms'>Number of atoms</option>
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63 <option value='bonds'>Number of bonds</option>
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64 <option value='dbonds'>Number of double bonds</option>
7
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65 <option value='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</option>
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66 <option value='HBD'>Number of hydrogen bond donors (JoelLib)</option>
0
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67 <option value='L5'>Lipinski Rule of Five</option>
7
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68 <option value='logP'>Octanol/water partition coefficient</option>
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69 <option value='MR'>Molar refractivity</option>
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70 <option value='nF'>Number of fluorine atoms</option>
0
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71 <option value='sbonds'>Number of single bonds</option>
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72 <option value='tbonds'>Number of triple bonds</option>
7
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73 <option value='TPSA'>Topological polar surface area</option>
0
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74 </param>
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75
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76 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
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77 <option value='svg'>SVG</option>
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78 <option value='png'>PNG</option>
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79 </param>
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80
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81 </inputs>
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82 <outputs>
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83 <data name="outfile" format="png" label="${tool.name} on ${on_string}">
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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84 <change_format>
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85 <when input="oformat" value="svg" format="svg"/>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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86 </change_format>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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91 <param name="infile" ftype="smi" value="8_mol.smi" />
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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92 <param name="embed_molecule_as_cml" value="False" />
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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93 <param name="draw_all_carbon_atoms" value="True" />
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94 <param name="thick_lines" value="True" />
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95 <param name='display_name' value="title" />
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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96 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" lines_diff="100" />
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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97 </test>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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98 </tests>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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99 <help>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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100 <![CDATA[
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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101
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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102 .. class:: infomark
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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103
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104 **What this tool does**
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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105
7
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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.
0
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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107
15
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108 .. _PNG: https://open-babel.readthedocs.io/en/latest/FileFormats/PNG_2D_depiction.html
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109 .. _SVG: https://open-babel.readthedocs.io/en/latest/FileFormats/SVG_2D_depiction.html
0
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110
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111 -----
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112
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113 .. class:: warningmark
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114
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115 **Hint**
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116
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117 Use only libraries with at most a few hundred molecules.
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118
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119
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120 ]]>
88f229c63734 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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121 </help>
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122 <expand macro="citations"/>
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123 </tool>