--- a/gene_family_integrator.py	Fri Apr 07 16:30:51 2017 -0400
+++ b/gene_family_integrator.py	Mon Apr 10 11:30:34 2017 -0400
@@ -8,7 +8,7 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
-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('--orthogroup_fna', dest='orthogroup_fna', default=None, help='Use correspong coding sequences')
 parser.add_argument('--output', dest='output', help="Output dataset")
@@ -27,5 +27,5 @@
 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
 rc = proc.wait()
 utils.check_execution_errors(rc, proc.stderr)
-utils.move_directory_files(OUTPUT_DIR, args.output_dir)
+utils.move_directory_files(os.path.join(OUTPUT_DIR, 'orthogroups_fasta'), args.output_dir)
 utils.write_html_output(args.output, 'Integrated gene family sequences', args.output_dir)

--- a/gene_family_integrator.xml	Fri Apr 07 16:30:51 2017 -0400
+++ b/gene_family_integrator.xml	Mon Apr 10 11:30:34 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="0.8.0">
+<tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.0">
     <description>integrates de novo assembly sequences with scaffold gene family sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -60,8 +60,10 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
         <test>
         </test>
+        -->
     </tests>
     <help>
 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary

--- a/macros.xml	Fri Apr 07 16:30:51 2017 -0400
+++ b/macros.xml	Mon Apr 10 11:30:34 2017 -0400
@@ -1,5 +1,6 @@
 <?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>
@@ -25,6 +26,11 @@
             <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:"/>
@@ -86,7 +92,7 @@
             <when value="yes">
                 <conditional name="trim_type_cond">
                     <param name="trim_type" type="select" label="Select process used for gap trimming">
-                        <option value="gap_trimming" selected="true">Nucleotide based </option>
+                        <option value="gap_trimming" selected="true">Nucleotide based</option>
                         <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
                     </param>
                     <when value="gap_trimming">