--- 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.