--- a/gene_family_aligner.py	Mon Apr 10 10:55:45 2017 -0400
+++ b/gene_family_aligner.py	Mon Apr 10 12:47:18 2017 -0400
@@ -13,23 +13,19 @@
 parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
 parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
 parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=None, help='"Maximum number of iterations')
-parser.add_argument('--method', dest='method', help='Protein clustering method')
 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
 parser.add_argument('--output', dest='output', help="Output dataset")
-parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory")
+parser.add_argument('--output_dir', dest='output_dir', help="Output dataset files_path directory")
 parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute')
 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
 parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')
-parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
 
 args = parser.parse_args()
 
 # Build the command line.
 cmd = 'GeneFamilyAligner'
 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
-cmd += ' --scaffold %s' % args.scaffold
-cmd += ' --method %s' % args.method
 cmd += ' --alignment_method %s' % args.alignment_method
 if args.alignment_method == 'pasta':
     if args.pasta_script_path is not None:

--- a/gene_family_aligner.xml	Mon Apr 10 10:55:45 2017 -0400
+++ b/gene_family_aligner.xml	Mon Apr 10 12:47:18 2017 -0400
@@ -8,13 +8,10 @@
     <command>
         <![CDATA[
             #set input_format = $input_format_cond.input_format
-            #set scaffold = $input_format_cond.scaffold
             #set alignment_method_cond = $input_format_cond.alignment_method_cond
             #set alignment_method = $alignment_method_cond.alignment_method
 
             python $__tool_directory__/gene_family_aligner.py
-            --scaffold '$scaffold.fields.path'
-            --method $input_format_cond.method
             --alignment_method $alignment_method
             #if str($alignment_method) == 'pasta':
                 --pasta_script_path '$__tool_directory__/run_pasta.py'
@@ -71,14 +68,10 @@
             </param>
             <when value="ptortho">
                 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
-                <expand macro="param_scaffold" />
-                <expand macro="param_method" />
                 <expand macro="cond_alignment_method" />
             </when>
             <when value="ptorthocs">
                 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
-                <expand macro="param_scaffold" />
-                <expand macro="param_method" />
                 <expand macro="cond_alignment_method" />
                 <expand macro="param_codon_alignments" />
             </when>
@@ -123,9 +116,6 @@
 
     - **Construct orthogroup multiple codon alignments** - construct orthogroup multiple codon alignments.
 
- * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
- * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
-
  * **Select method for multiple sequence alignments**
 
   - **MAFFT algorithm** - mafft algorithm.

--- a/macros.xml	Mon Apr 10 10:55:45 2017 -0400
+++ b/macros.xml	Mon Apr 10 12:47:18 2017 -0400
@@ -92,7 +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">