--- a/gene_family_classifier.xml	Mon Feb 13 09:11:32 2017 -0500
+++ b/gene_family_classifier.xml	Wed Feb 15 11:16:24 2017 -0500
@@ -51,7 +51,6 @@
                 #if str($specify_single_copy) == 'yes':
                     #set single_copy_orthogroup = True
                     #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
-                    ## FixMe: the single_copy_custom option is not currently supported.
                     #set single_copy = $single_copy_cond.single_copy
                     #if $create_ortho_sequences:
                         #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
@@ -73,6 +72,7 @@
             --scaffold '$scaffold.fields.path'
             --method $method
             --classifier $save_hmmscan_log_cond.classifier
+            --config_dir '$scaffold.fields.config_path'
             --num_threads \${GALAXY_SLOTS:-4}
 
             #if str($options_type.options_type_selector) == 'advanced':
@@ -80,8 +80,12 @@
                     --super_orthogroups $super_orthogroups
                 #end if
                 #if $single_copy_orthogroup:
-                    --single_copy_taxa $single_copy_cond.single_copy_taxa
-                    --taxa_present $single_copy_cond.taxa_present
+                    #if str($single_copy) == 'custom':
+                        --single_copy_custom
+                    #else:
+                        --single_copy_taxa $single_copy_cond.single_copy_taxa
+                        --taxa_present $single_copy_cond.taxa_present
+                    #end if
                 #end if
                 #if str($create_orthogroup) == 'yes':
                     --orthogroup_fasta
@@ -180,16 +184,10 @@
                     <when value="yes">
                         <conditional name="single_copy_cond">
                             <param name="single_copy" type="select" label="Select single copy configuration">
-                                <!--
-                                FixMe: single_copy_custom is not currently supported because the
-                                ~/config/*.singleCopy.config files are not easy to manage by a suer
-                                and the GeneFamilyClassifier pipeline must be enhanced to provide an
-                                optional parameter for the hard-coded path to the config.
-                                <option value="custom" selected="true">Single copy orthogroup custom</option>
-                                -->
+                                <option value="custom" selected="true">Single copy orthogroup custom configuration</option>
                                 <option value="taxa">Minimum single copy taxa required in orthogroup</option>
                             </param>
-                            <when value="custom" />
+                            <when value="custom"/>
                             <when value="taxa">
                                 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/>
                                 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/>