diff ob_depiction_svg.xml @ 0:88f229c63734 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ob_depiction_svg.xml	Sat May 20 08:38:05 2017 -0400
@@ -0,0 +1,125 @@
+<tool id="openbabel_svg_depiction" name="Visualisation" version="@VERSION@.0">
+    <description>of compounds</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive">
+<![CDATA[
+    obabel
+        -i${infile.ext}
+        "${infile}"
+        $embed_molecule_as_cml
+        $draw_all_carbon_atoms
+        -xC
+        -O
+        "${outfile}"
+        -o$oformat
+        #if $sort:
+            --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>
+        <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='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' optional="True" label="Sorting the displayed molecules 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='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" 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="False" />
+            <param name="draw_all_carbon_atoms" value="True" />
+            <param name="thick_lines" value="True" />
+            <param name='display_name' value="title" />
+            <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" lines_diff="100" />
+        </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.
+
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>