# HG changeset patch
# User bgruening
# Date 1586441391 14400
# Node ID 340f8d63c1f46c2ba64107992e8058ca7b178cac
# Parent  da0059ee548ad21e2ab2dbf79884812c5b2cb320
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"

diff -r da0059ee548a -r 340f8d63c1f4 macros.xml
--- a/macros.xml	Wed Mar 25 16:49:41 2020 -0400
+++ b/macros.xml	Thu Apr 09 10:09:51 2020 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">2.4.2.1</token>
+    <token name="@VERSION@">2.4.2.2</token>
 
     <xml name="requirements">
         <requirements>
diff -r da0059ee548a -r 340f8d63c1f4 ob_filter.py
--- a/ob_filter.py	Wed Mar 25 16:49:41 2020 -0400
+++ b/ob_filter.py	Thu Apr 09 10:09:51 2020 -0400
@@ -40,7 +40,7 @@
     for mol in pybel.readfile('sdf', args.input):
         for key, elem in filters.items():
             # map the short description to the larger metadata names stored in the sdf file
-            property = cheminfolib.ColumnNames[key]
+            property = cheminfolib.ColumnNames.get(key, key)
             min = elem[0]
             max = elem[1]
             if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max):
@@ -113,7 +113,7 @@
         # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
         mol = next(pybel.readfile('sdf', args.input))
         for key, elem in filters.items():
-            property = cheminfolib.ColumnNames[key]
+            property = cheminfolib.ColumnNames.get(key, key)
             if not property in mol.data:
                 break
         else:
diff -r da0059ee548a -r 340f8d63c1f4 ob_filter.xml
--- a/ob_filter.xml	Wed Mar 25 16:49:41 2020 -0400
+++ b/ob_filter.xml	Thu Apr 09 10:09:51 2020 -0400
@@ -10,40 +10,45 @@
     python '$__tool_directory__/ob_filter.py'
       -i '${infile}'
       -o '${outfile}'
-      -iformat '${infile.ext}'
-      -oformat '${infile.ext}'
+      -iformat "${infile.ext}"
+      -oformat "${infile.ext}"
       #if $filter_methods.filter_methods_opts == "__filter_by_name__":
           --list_of_names '$name_file'
           --filters '__filter_by_name__'
       #else
-          --filters '{
-            #if $filter_methods.filter_methods_opts == "ruleof5":
-              "hbd" : [0, 5],
-              "hba" : [0, 10],
-              "molwt" : [0, 500],
-              "logp" : [-5, 5],
-            #elif $filter_methods.filter_methods_opts == "LeadLike":
-              "rotbonds" : [0, 7],
-              "molwt" : [0, 350],
-              "logp" : [-5, 3.5],
-            #elif $filter_methods.filter_methods_opts == "DrugLike":
-              "hba" : [0, 10],
-              "rotbonds" : [0, 8],
-              "molwt" : [150, 500],
-              "logp" : [-5, 5],
-              "psa" : [0, 150],
-            #elif $filter_methods.filter_methods_opts == "FragmentLike":
-              "rotbonds" : [0, 5],
-              "molwt" : [0, 250],
-              "logp" : [-5, 2.5],
-            #else:
-              #for $filter in $filter_methods.filter_set:
+        --filters '{
+          #if $filter_methods.filter_methods_opts == "ruleof5":
+            "hbd" : [0, 5],
+            "hba" : [0, 10],
+            "molwt" : [0, 500],
+            "logp" : [-5, 5],
+          #elif $filter_methods.filter_methods_opts == "LeadLike":
+            "rotbonds" : [0, 7],
+            "molwt" : [0, 350],
+            "logp" : [-5, 3.5],
+          #elif $filter_methods.filter_methods_opts == "DrugLike":
+            "hba" : [0, 10],
+            "rotbonds" : [0, 8],
+            "molwt" : [150, 500],
+            "logp" : [-5, 5],
+            "psa" : [0, 150],
+          #elif $filter_methods.filter_methods_opts == "FragmentLike":
+            "rotbonds" : [0, 5],
+            "molwt" : [0, 250],
+            "logp" : [-5, 2.5],
+          #else:
+            #for $filter in $filter_methods.filter_set:
+              #if $filter.filter_sel.filter_sel_opts == "field":
+                #set $filter_selected = $filter.filter_sel['field_name']
+                "$filter_selected": [$filter.filter_sel['field_min'], $filter.filter_sel['field_max'] ],
+              #else:
                 #set $filter_selected = $filter.filter_sel.filter_sel_opts
                 #set $filter_min = $filter_selected + "_min"
                 #set $filter_max = $filter_selected + "_max"
                 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
-              #end for
-            #end if
+              #end if
+            #end for
+          #end if
           }'
         #end if
 ]]>
@@ -80,6 +85,7 @@
               <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>
+              <option value="field">Filter by a user-defined SDF property</option>
               <!-- Add later, we need to add a new smarts pattern to plugindefines.txt
               <option value="hatoms">Number of heavy atoms</option>-->
               <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html -->
@@ -117,6 +123,19 @@
               <param name="atoms_min" type="integer" value="" label="Minimum number of atoms"/>
               <param name="atoms_max" type="integer" value="" label="Maximum number of atoms"/>
             </when>
+            <when value="field">
+              <param name="field_name" type="text" value="" label="Name of the SDF property to filter by">
+                <sanitizer invalid_char="">
+                  <valid initial="string.ascii_letters,string.digits">
+                    <add value="_" />
+                    <add value="." />
+                    <add value=" " />
+                  </valid>
+                </sanitizer>
+              </param>
+              <param name="field_min" type="integer" value="" label="Minimum value"/>
+              <param name="field_max" type="integer" value="" label="Maximum value"/>
+            </when>
             <!--<when value="rings">
               <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
               <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
@@ -141,6 +160,15 @@
         <param name="filter_methods_opts" value="ruleof5" />
         <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
     </test>
+    <test>
+        <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
+        <param name="filter_methods_opts" value="user" />
+        <param name="filter_sel_opts" value="field" />
+        <param name="field_name" value="PUBCHEM_EXACT_MASS"/>
+        <param name="field_min" value="100"/>
+        <param name="field_max" value="200"/>
+        <output name="outfile" ftype="sdf" file="ob_filter_on_CID2244.sdf" lines_diff="2"/>
+    </test>
     <!--
     Limitation of the test framework:
     https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820