# HG changeset patch
# User greg
# Date 1490109788 14400
# Node ID 72341ff03a1531c6ae2b989152191b90428807a3
# Parent  c840726bd580eebb392ea9e65ff6ec94eb01eea2
Uploaded

diff -r c840726bd580 -r 72341ff03a15 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Mar 21 11:08:38 2017 -0400
+++ b/gene_family_classifier.xml	Tue Mar 21 11:23:08 2017 -0400
@@ -73,10 +73,10 @@
                             --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
                         #end if
                     #else:
-                        #if str($single_copy_cond.single_copy_taxa) != '':
+                        #if str($single_copy_cond.single_copy_taxa) >= 0:
                             --single_copy_taxa $single_copy_cond.single_copy_taxa
                         #end if
-                        #if str($single_copy_cond.taxa_present) != '':
+                        #if str($single_copy_cond.taxa_present) >= 0:
                             --taxa_present $single_copy_cond.taxa_present
                         #end if
                     #end if
@@ -185,8 +185,8 @@
                                 </conditional>
                             </when>
                             <when value="taxa">
-                                <param name="single_copy_taxa" type="integer" optional="true" label="Minimum single copy taxa"/>
-                                <param name="taxa_present" type="integer" optional="true" label="Minimum taxa present"/>
+                                <param name="single_copy_taxa" type="integer" value="-1" label="Minimum single copy taxa" help="Negative values have no affect"/>
+                                <param name="taxa_present" type="integer" value="-1" label="Minimum taxa present" help="Negative values have no affect"/>
                             </when>
                         </conditional>
                     </when>
@@ -281,7 +281,7 @@
 
        * **Custom selection file** - select a single/low-copy customized configuration file from your history.
 
-     * **Global selection configuration**
+     * **Global selection configuration** - the upper limit values of the folowing 2 parameters vary depending on the selected gene family scaffold, and the tool will produce an error if the value exceeds the number of species in the circumscribed scaffold.  Negative values have no affect.
 
        * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup.
        * **Minimum taxa present** - minimum number of taxa present in the orthogroup.