# HG changeset patch
# User greg
# Date 1486581916 18000
# Node ID 3b2d35b7526814fb4ca95fb2dd9c86ce355a26f4
# Parent  a3b7f34ad3f7c3c85c76433806214ab2098d96a7
Uploaded

diff -r a3b7f34ad3f7 -r 3b2d35b75268 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Feb 08 11:17:10 2017 -0500
+++ b/gene_family_classifier.xml	Wed Feb 08 14:25:16 2017 -0500
@@ -19,11 +19,20 @@
             #set scaffold_selection = $os.path.split($scaffold_path)[1]
 
             #if str($options_type.options_type_selector) == 'advanced':
+                #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
+                #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
                 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
                 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
                 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
                 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
 
+                #if str($specify_super_orthogroups) == 'yes':
+                    #set specify_super_orthos = True
+                    #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
+                #else:
+                    #set specify_super_orthos = False
+                #end if
+
                 #if str($specify_single_copy) == 'yes':
                     #set single_copy_orthogroup = True
                     #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
@@ -68,7 +77,9 @@
             --num_threads \${GALAXY_SLOTS:-4}
 
             #if str($options_type.options_type_selector) == 'advanced':
-                --super_orthogroups $options_type.super_orthogroups
+                #if specify_super_orthos:
+                    --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
@@ -147,10 +158,19 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="super_orthogroups" type="select" label="Super Orthogroups" help="Secondary MCL clusters of orthogroups">
-                    <option value="min_evalue" selected="true">Minimum e-value</option>
-                    <option value="avg_evalue">Average e-value</option>
-                </param>
+                <conditional name="specify_super_orthogroups_cond">
+                    <param name="specify_super_orthogroups" type="select" label="Specify super orthogroups?" help="Secondary MCL clusters of orthogroups">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="super_orthogroups" type="select" label="Super Orthogroups">
+                            <option value="min_evalue" selected="true">Minimum e-value</option>
+                            <option value="avg_evalue">Average e-value</option>
+                        </param>
+                    </when>
+                </conditional>
                 <conditional name="specify_single_copy_cond">
                     <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?">
                         <option value="no" selected="true">No</option>