Mercurial > repos > bgruening > openbabel
diff visualisation/ob_depiction_svg.xml @ 2:125da3a296ca draft default tip
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| author | bgruening |
|---|---|
| date | Wed, 15 Jul 2015 12:13:08 -0400 |
| parents | 527ecd2fc500 |
| children |
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--- a/visualisation/ob_depiction_svg.xml Wed Aug 21 03:06:02 2013 -0400 +++ b/visualisation/ob_depiction_svg.xml Wed Jul 15 12:13:08 2015 -0400 @@ -1,127 +1,131 @@ -<tool id="ctb_ob_svg_depiction" name="Visualisation"> - <description>of compounds</description> - <requirements> - <requirement type="package" version="2.3.2">openbabel</requirement> - </requirements> - <command> - obabel -i${infile.ext} $infile - $embed_molecule_as_cml - $draw_all_carbon_atoms - -xC - -O - $outfile -o$oformat - #if str($sort) != "none": - --sort $sort - #end if - #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': - --append "$display_name" - --title "" - #end if - $thick_lines - 2>&1 - </command> - <inputs> - <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> - <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='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> - <option value='abonds'>Number of aromatic bonds</option> - <option value='atoms'>Number of atoms</option> - <option value='bonds'>Number of bonds</option> - <option value='cansmi'>Canonical SMILES</option> - <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='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='s'>SMARTS filter</option> - <option value='sbonds'>Number of single bonds</option> - <option value='smarts'>SMARTS filter</option> - <option value='tbonds'>Number of triple bonds</option> - <option value='TPSA'>topological polar surface area</option> - </param> - - <param name='sort' type='select' format='text' label="Sorting the displayed molecules by"> - <option value='none'>No sorting</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> - <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='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='sbonds'>Number of single bonds</option> - <option value='tbonds'>Number of triple bonds</option> - <option value='TPSA'>topological polar surface area</option> - </param> - - <param name='oformat' type='select' format='text' label="Format of the resulting picture"> - <option value='svg'>SVG</option> - <option value='png'>PNG</option> - </param> - - </inputs> - <outputs> - <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}"> - <change_format> - <when input="oformat" value="svg" format="svg"/> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="infile" ftype="smi" value="8_mol.smi" /> - <param name="embed_molecule_as_cml" value="" /> - <param name="draw_all_carbon_atoms" value="-a" /> - <param name="thick_lines" value="-xt" /> - <param name='display_name' value="title" /> - <param name='sort' value='none' /> - <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> - </test> - </tests> - <help> - -.. class:: infomark - -**What this tool does** - -Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction. - -.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html -.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html - ------ - -.. class:: warningmark - -**Hint** - -Use only libraries with at most a few hundred molecules. - ------ - -.. class:: infomark - -**Cite** - -`Open Babel`_ - -.. _Open Babel: http://openbabel.org/wiki/Main_Page - - </help> -</tool> +<tool id="ctb_ob_svg_depiction" name="Visualisation"> + <description>of compounds</description> + <requirements> + <requirement type="package" version="2.3.2">openbabel</requirement> + </requirements> + <command> +<![CDATA[ + obabel -i${infile.ext} $infile + $embed_molecule_as_cml + $draw_all_carbon_atoms + -xC + -O + $outfile -o$oformat + #if str($sort) != "none": + --sort $sort + #end if + #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': + --append "$display_name" + --title "" + #end if + $thick_lines + 2>&1 +]]> + </command> + <inputs> + <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> + <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='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> + <option value='abonds'>Number of aromatic bonds</option> + <option value='atoms'>Number of atoms</option> + <option value='bonds'>Number of bonds</option> + <option value='cansmi'>Canonical SMILES</option> + <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='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='s'>SMARTS filter</option> + <option value='sbonds'>Number of single bonds</option> + <option value='smarts'>SMARTS filter</option> + <option value='tbonds'>Number of triple bonds</option> + <option value='TPSA'>topological polar surface area</option> + </param> + + <param name='sort' type='select' format='text' label="Sorting the displayed molecules by"> + <option value='none'>No sorting</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> + <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='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='sbonds'>Number of single bonds</option> + <option value='tbonds'>Number of triple bonds</option> + <option value='TPSA'>topological polar surface area</option> + </param> + + <param name='oformat' type='select' format='text' label="Format of the resulting picture"> + <option value='svg'>SVG</option> + <option value='png'>PNG</option> + </param> + + </inputs> + <outputs> + <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}"> + <change_format> + <when input="oformat" value="svg" format="svg"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="infile" ftype="smi" value="8_mol.smi" /> + <param name="embed_molecule_as_cml" value="" /> + <param name="draw_all_carbon_atoms" value="-a" /> + <param name="thick_lines" value="-xt" /> + <param name='display_name' value="title" /> + <param name='sort' value='none' /> + <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> + </test> + </tests> + <help> +<![CDATA[ + +.. class:: infomark + +**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. + +.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html +.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html + +----- + +.. class:: warningmark + +**Hint** + +Use only libraries with at most a few hundred molecules. + +----- + +.. class:: infomark + +**Cite** + +`Open Babel`_ + +.. _Open Babel: http://openbabel.org/wiki/Main_Page + +]]> + </help> +</tool>