# HG changeset patch
# User bgruening
# Date 1557250526 14400
# Node ID f93f3e01abe8d2ffcb0814db229c5e3b2a2cde7f
# Parent  0b9ee280c4392e2d2ed938e4699d4f0319effb9a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e

diff -r 0b9ee280c439 -r f93f3e01abe8 macros.xml
--- a/macros.xml	Mon Sep 03 16:41:49 2018 -0400
+++ b/macros.xml	Tue May 07 13:35:26 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>
-
-
-
diff -r 0b9ee280c439 -r f93f3e01abe8 ob_spectrophore_search.xml
--- a/ob_spectrophore_search.xml	Mon Sep 03 16:41:49 2018 -0400
+++ b/ob_spectrophore_search.xml	Tue May 07 13:35:26 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="openbabel_spectrophore_search" name="Spectrophores(TM) search:" version="@VERSION@.0">
-    <description>similarity search based on 1D chemical features</description>
+<tool id="openbabel_spectrophore_search" name="Spectrophores search" version="@VERSION@.0">
+    <description>- similarity search based on 1D chemical features</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.7.1">numpy</requirement>
+        <requirement type="package" version="1.16.2">numpy</requirement>
     </expand>
     <command detect_errors="aggressive">
 <![CDATA[
@@ -17,10 +17,10 @@
     </command>
     <inputs>
         <param name="target" type="data" format="sdf"
-            label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/>
+            label="Target molecule in SDF format (it must contain Spectrophores stored as meta-data)"/>
         <param name="library" type="data" format="tabular"
-            label="Tabular file with pre-computed Spectrophores(TM) in one column"/>
-        <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors"
+            label="Tabular file with pre-computed Spectrophores in one column"/>
+        <param name="column" label="Specify the column number containing the Spectrophores descriptors"
             type="data_column" data_ref="library" accept_default="true" />
     </inputs>
     <outputs>
@@ -41,10 +41,10 @@
 
 **What does this tool do?**
 
-This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library.
+This tool computes the Euclidean distance between the |Spectrophores (TM)| descriptors of the target to each molecule stored in the library.
 
 |Spectrophores (TM)| search
-		|Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of |Spectrophores (TM)| of different molecules.
+		|Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows easy comparison of |Spectrophores (TM)| of different molecules.
 
 		Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.
 
@@ -53,15 +53,14 @@
 - |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors
 - |Spectrophores (TM)| can be applied in both a ligand- or target-based setting
 - |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds
-- |Spectrophores (TM)| can be computed fast
+- |Spectrophores (TM)| can be computed rapidly
 
-.. |Spectrophores (TM)| unicode:: Spectrophores U+2122
 
 -----
 
 .. class:: warningmark
 
-**Hint** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.
+**Hint:** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.
 
 -----
 
@@ -91,6 +90,7 @@
 
 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
+.. |Spectrophores (TM)| unicode:: Spectrophores U+2122
 
 ]]>
     </help>
diff -r 0b9ee280c439 -r f93f3e01abe8 test-data/2_mol.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_mol.dat	Tue May 07 13:35:26 2019 -0400
@@ -0,0 +1,2 @@
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
diff -r 0b9ee280c439 -r f93f3e01abe8 test-data/CO.smarts
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CO.smarts	Tue May 07 13:35:26 2019 -0400
@@ -0,0 +1,1 @@
+CO