# HG changeset patch
# User bgruening
# Date 1557250505 14400
# Node ID 0e382252d23d55659aa36546935236538ee2ab86
# Parent  69e02cf8885686cb82778df305a710ec527fe52c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e

diff -r 69e02cf88856 -r 0e382252d23d macros.xml
--- a/macros.xml	Mon Sep 03 16:42:58 2018 -0400
+++ b/macros.xml	Tue May 07 13:35:05 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 69e02cf88856 -r 0e382252d23d ob_filter.xml
--- a/ob_filter.xml	Mon Sep 03 16:42:58 2018 -0400
+++ b/ob_filter.xml	Tue May 07 13:35:05 2019 -0400
@@ -45,7 +45,7 @@
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
-        label="Select input file previously annotated with the 'Compute physico-chemical properties' tool"/>
+        label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
     <conditional name="filter_methods">
       <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
         <option value="user">User-defined properties</option>
@@ -59,16 +59,16 @@
       <when value="DrugLike" />
       <when value="FragmentLike" />
       <when value="user">
-        <repeat name="filter_set" title="Filters selection">
+        <repeat name="filter_set" title="Select custom filters">
           <conditional name="filter_sel">
             <param name="filter_sel_opts" type="select" label="Select properties to filter">
-              <option value="hbd">Number of Hydrogen-bond donor groups</option>
-              <option value="hba">Number of Hydrogen-bond acceptor groups</option>
-              <option value="psa">Total polar Surface Area</option>
+              <option value="hbd">Number of hydrogen-bond donor groups</option>
+              <option value="hba">Number of hydrogen-bond acceptor groups</option>
+              <option value="psa">Total polar surface area</option>
               <option value="rotbonds">Number of rotatable bonds</option>
               <option value="molwt">Molecular weight</option>
-              <option value="logp">Predicted value of LogP</option>
-              <option value="mr">Predicted value for the Molecular Refractivity</option>
+              <option value="logp">Predicted value of logP</option>
+              <option value="mr">Predicted value for the molecular refractivity</option>
               <option value="atoms">Number of atoms</option>
               <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
               <option value="hatoms">Number of heavy atoms</option>-->
@@ -76,32 +76,32 @@
               <!--<option value="rings">Number of rings</option>-->
             </param>
             <when value="hbd">
-              <param name="hbd_min" type="integer" value="" label="Minimum number of HB donors"/>
-              <param name="hbd_max" type="integer" value="" label="Maximum number of HB donors"/>
+              <param name="hbd_min" type="integer" value="" label="Minimum number of hydrogen bond donors"/>
+              <param name="hbd_max" type="integer" value="" label="Maximum number of hydrogen bond donors"/>
             </when>
             <when value="hba">
-              <param name="hba_min" type="integer" value="" label="Minimum number of HB acceptors"/>
-              <param name="hba_max" type="integer" value="" label="Maximum number of HB acceptors"/>
+              <param name="hba_min" type="integer" value="" label="Minimum number of hydrogen bond acceptors"/>
+              <param name="hba_max" type="integer" value="" label="Maximum number of hydrogen bond acceptors"/>
             </when>
             <when value="psa">
-              <param name="psa_min" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/>
-              <param name="psa_max" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/>
+              <param name="psa_min" type="integer" value="" label="Minimum threshold for the total polar surface area"/>
+              <param name="psa_max" type="integer" value="" label="Maximum threshold for the total polar surface area"/>
             </when>
             <when value="rotbonds">
               <param name="rotbonds_min" type="integer" value="" label="Minimum number of rotatable bonds"/>
               <param name="rotbonds_max" type="integer" value="" label="Maximum number of rotatable bonds"/>
             </when>
             <when value="molwt">
-              <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/>
-              <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/>
+              <param name="molwt_min" type="integer" value="" label="Minimum threshold value for the molecular weight"/>
+              <param name="molwt_max" type="integer" value="" label="Maximum threshold value for the molecular weight"/>
             </when>
             <when value="logp">
-              <param name="logp_min" type="float" value="" label="Minimum threshold value for the log-P"/>
-              <param name="logp_max" type="float" value="" label="Maximum threshold value for the log-P"/>
+              <param name="logp_min" type="float" value="" label="Minimum threshold value for log P"/>
+              <param name="logp_max" type="float" value="" label="Maximum threshold value for log P"/>
             </when>
             <when value="mr">
-              <param name="mr_min" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/>
-              <param name="mr_max" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/>
+              <param name="mr_min" type="float" value="" label="Minimum threshold value for the molecular refractivity"/>
+              <param name="mr_max" type="float" value="" label="Maximum threshold value for the molecular refractivity"/>
             </when>
             <when value="atoms">
               <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
@@ -154,9 +154,9 @@
 
 **Hint**
 
-| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
+| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. This should be faster and the file can be reused, although it is larger than a SMILES file.
 |
-| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
+| For exact matches use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
 |
 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
 
diff -r 69e02cf88856 -r 0e382252d23d test-data/2_mol.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_mol.dat	Tue May 07 13:35:05 2019 -0400
@@ -0,0 +1,2 @@
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
+CC(=O)OC1=CC=CC=C1C(=O)[O-]
diff -r 69e02cf88856 -r 0e382252d23d test-data/CO.smarts
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CO.smarts	Tue May 07 13:35:05 2019 -0400
@@ -0,0 +1,1 @@
+CO