Mercurial > repos > bgruening > openbabel_svg_depiction

changeset 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 ed50b83b02e9
children 136ceea822f5
files macros.xml ob_depiction_svg.xml test-data/2_mol.dat test-data/CO.smarts
diffstat 4 files changed, 24 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Sep 03 16:41:32 2018 -0400
+++ b/macros.xml	Tue May 07 13:35:51 2019 -0400
@@ -1,9 +1,10 @@
 <macros>
-    <token name="@VERSION@">2.4.1</token>
+    <token name="@VERSION@">2.4.2</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.4.1">openbabel</requirement>
+            <requirement type="package" version="3">python</requirement>
             <yield />
         </requirements>
     </xml>
@@ -37,6 +38,3 @@
         </citations>
     </xml>
 </macros>
-
-
-
--- a/ob_depiction_svg.xml	Mon Sep 03 16:41:32 2018 -0400
+++ b/ob_depiction_svg.xml	Tue May 07 13:35:51 2019 -0400
@@ -29,12 +29,12 @@
     <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="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>
+        <param name='display_name' type='select' format='text' label="Property to display under the molecule">
+            <option value='title'>Molecule 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>
@@ -42,14 +42,13 @@
             <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='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</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='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>
@@ -57,22 +56,21 @@
             <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>
+        <param name='sort' type='select' format='text' optional="True" label="Sort the displayed molecules (if input contains more than one) 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='HBA1'>Number of hydrogen bond acceptors (JoelLib 1)</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='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>
+            <option value='TPSA'>Topological polar surface area</option>
         </param>
 
         <param name='oformat' type='select' format='text' label="Format of the resulting picture">
@@ -105,7 +103,7 @@
 
 **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.
+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.
 
 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_mol.dat	Tue May 07 13:35:51 2019 -0400
@@ -0,0 +1,2 @@
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CO.smarts	Tue May 07 13:35:51 2019 -0400
@@ -0,0 +1,1 @@
+CO