--- a/gene_family_classifier.py	Fri Apr 07 08:38:49 2017 -0400
+++ b/gene_family_classifier.py	Tue Apr 11 14:24:23 2017 -0400
@@ -12,15 +12,15 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--input', dest='input', help="Input dataset")
-parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
+parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--classifier', dest='classifier', help='Protein classification method')
 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
 parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification')
 parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration')
-parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=None, help='"Minimum single copy taxa required in orthogroup')
-parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=None, help='Minimum taxa required in single copy orthogroup')
+parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='"Minimum single copy taxa required in orthogroup')
+parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
@@ -47,9 +47,9 @@
     cmd += ' --super_orthogroups %s' % args.super_orthogroups
 if args.single_copy_custom is not None:
     cmd += ' --single_copy_custom %s' % args.single_copy_custom
-if args.single_copy_taxa is not None:
+if args.single_copy_taxa > 0:
     cmd += ' --single_copy_taxa %d' % args.single_copy_taxa
-if args.taxa_present is not None:
+if args.taxa_present > 0:
     cmd += ' --taxa_present %d' % args.taxa_present
 if args.orthogroup_fasta is None:
     create_ortho_sequences = False

--- a/gene_family_classifier.xml	Fri Apr 07 08:38:49 2017 -0400
+++ b/gene_family_classifier.xml	Tue Apr 11 14:24:23 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="0.4.0">
+<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.0">
     <description>classifies gene sequences into pre-computed orthologous plant gene family clusters</description>
     <macros>
         <import>macros.xml</import>
@@ -67,10 +67,10 @@
                             --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config'
                         #end if
                     #else:
-                        #if $single_copy_cond.single_copy_taxa > 0:
+                        #if str($single_copy_cond.single_copy_taxa):
                             --single_copy_taxa $single_copy_cond.single_copy_taxa
                         #end if
-                        #if $single_copy_cond.taxa_present > 0:
+                        #if str($single_copy_cond.taxa_present):
                             --taxa_present $single_copy_cond.taxa_present
                         #end if
                     #end if
@@ -180,8 +180,8 @@
                                 </conditional>
                             </when>
                             <when value="taxa">
-                                <param name="single_copy_taxa" type="integer" value="0" min="0" label="Minimum single copy taxa" help="Zero values have no affect"/>
-                                <param name="taxa_present" type="integer" value="0" min="0" label="Minimum taxa present" help="Zero values have no affect"/>
+                                <param name="single_copy_taxa" type="integer" optional="true" min="0" label="Minimum single copy taxa"/>
+                                <param name="taxa_present" type="integer" optional="true" min="0" label="Minimum taxa present"/>
                             </when>
                         </conditional>
                     </when>
@@ -272,7 +272,7 @@
 
    * **Selection criterion** - single/low-copy orthogroups selection criterion. PlantTribes provides custom and global selection criteria for selecting user-defined single/low-copy scaffold orthogoups.
 
-     * **Global selection configuration** - the upper limit values of the following two 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.  Zero values have no affect.
+     * **Global selection configuration** - the upper limit values of the following two 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.
 
        * **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.

--- a/macros.xml	Fri Apr 07 08:38:49 2017 -0400
+++ b/macros.xml	Tue Apr 11 14:24:23 2017 -0400
@@ -1,10 +1,16 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
+    <token name="@WRAPPER_VERSION@">0.8</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
             <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
         </requirements>
     </xml>
+    <xml name="requirements_gene_family_aligner">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
+        </requirements>
+    </xml>
     <xml name="requirements_gene_family_classifier">
         <requirements>
             <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
@@ -15,6 +21,16 @@
             <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
         </requirements>
     </xml>
+    <xml name="requirements_kaks_analysis">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_phylogeny_builder">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
+        </requirements>
+    </xml>
     <xml name="stdio">
         <stdio>
             <exit_code range="1:"/>
@@ -23,10 +39,10 @@
             <regex match="Exception:"/>
         </stdio>
     </xml>
-    <xml name="param_scaffold">
-        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
-            <options from_data_table="plant_tribes_scaffolds" />
-            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
+    <xml name="param_codon_alignments">
+        <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
         </param>
     </xml>
     <xml name="param_method">
@@ -36,12 +52,74 @@
             <option value="orthomcl">OrthoMCL</option>
         </param>
     </xml>
+    <xml name="param_options_type">
+        <param name="options_type" type="select" label="Options Configuration">
+            <option value="basic" selected="true">Basic</option>
+            <option value="advanced">Advanced</option>
+        </param>
+    </xml>
     <xml name="param_orthogroup_fna">
-        <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
+        <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
             <option value="yes" selected="true">Yes</option>
             <option value="no">No</option>
         </param>
     </xml>
+    <xml name="param_scaffold">
+        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
+            <options from_data_table="plant_tribes_scaffolds" />
+            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
+        </param>
+    </xml>
+    <xml name="param_sequence_type">
+        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
+            <option value="protein" selected="true">Amino acid based</option>
+            <option value="dna">Nucleotide based</option>
+        </param>
+    </xml>
+    <xml name="cond_alignment_method">
+        <conditional name="alignment_method_cond">
+            <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
+                <option value="mafft" selected="true">MAFFT algorithm</option>
+                <option value="pasta">PASTA algorithm</option>
+            </param>
+            <when value="mafft" />
+            <when value="pasta">
+                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="cond_remove_gappy_sequences">
+        <conditional name="remove_gappy_sequences_cond">
+            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <conditional name="trim_type_cond">
+                    <param name="trim_type" type="select" label="Select process used for trimming">
+                        <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
+                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
+                    </param>
+                    <when value="gap_trimming">
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
+                    </when>
+                    <when value="automated_trimming" />
+                </conditional>
+                <conditional name="remove_sequences_with_gaps_cond">
+                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </xml>
     <xml name="citation1">
         <citation type="bibtex">
             @misc{None,