# HG changeset patch
# User greg
# Date 1487348980 18000
# Node ID 850363a7e1aee267f52ecbf8e0593763722858cb
# Parent  0d689b9662ec04752fcbe5d637a4bdda895929f4
Uploaded

diff -r 0d689b9662ec -r 850363a7e1ae gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 16 08:37:13 2017 -0500
+++ b/gene_family_classifier.xml	Fri Feb 17 11:29:40 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.3">
+<tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.6.0">
     <description>into precomputed orthologous gene family clusters</description>
     <requirements>
-        <requirement type="package" version="0.3">plant_tribes_gene_family_classifier</requirement>
+        <requirement type="package" version="0.6">plant_tribes_gene_family_classifier</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -81,7 +81,14 @@
                 #end if
                 #if $single_copy_orthogroup:
                     #if str($single_copy) == 'custom':
-                        --single_copy_custom
+                        #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond
+                        #set single_copy_custom = $single_copy_custom_cond.single_copy_custom
+                        #if str($single_copy_custom) == 'no':
+                            #set single_copy_custom_config = $os.path.join($scaffold.fields.path, 'singleCopy.config')
+                            --single_copy_custom '$single_copy_custom_config'
+                        #else:
+                            --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
+                        #end if
                     #else:
                         --single_copy_taxa $single_copy_cond.single_copy_taxa
                         --taxa_present $single_copy_cond.taxa_present
@@ -187,7 +194,18 @@
                                 <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">
+                                <conditional name="single_copy_custom_cond">
+                                    <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration?" help="Select No to use the default configuration">
+                                        <option value="no" selected="true">No</option>
+                                        <option value="yes">Yes</option>
+                                    </param>
+                                    <when value="no"/>
+                                    <when value="yes">
+                                        <param name="single_copy_custom_config" format="txt" type="data" label="Select single copy custom configuration file"/>
+                                    </when>
+                                </conditional>
+                            </when>
                             <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"/>