--- a/gene_family_aligner.xml	Thu Oct 05 14:14:56 2017 -0400
+++ b/gene_family_aligner.xml	Mon Oct 09 08:56:27 2017 -0400
@@ -49,7 +49,7 @@
 #end if
     ]]></command>
     <inputs>
-        <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" />
+        <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
         <conditional name="alignment_method_cond">
             <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
                 <option value="mafft" selected="true">MAFFT</option>
@@ -92,7 +92,7 @@
                         <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
                     </when>
                 </conditional>
-                <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments">
+                <param name="output_pristine_alignments" type="select" display="radio" label="Output primary and intermediate alignemnts?" help="In addition to trimmed/filtered alignments">
                     <option value="no" selected="true">No</option>
                     <option value="yes">Yes</option>
                 </param>
@@ -146,7 +146,7 @@
 
 **Required options**
 
- * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history.  Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
+ * **Integrated orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyIntegrator tool selected from your history.  Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.
 
  * **Multiple sequence alignment method** - method for estimating orthogroup multiple sequence alignments.  PlantTribes estimates alignments using either MAFFT's L-INS-i algorithm or the divide and conquer approach implemented in the PASTA pipeline for large alignments.
 
@@ -168,7 +168,7 @@
 
     - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences.  Zero value has no effect.
 
- * **Output additional dataset collection of files** - selecting 'Yes' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools).
+ * **Output primary and intermediate alignments** - selecting 'Yes' will produce a dataset collection of primary and intermediate alignments, the elements of which can be viewed with viaula tools, in addition to the final trimmed and/or filtered alignments dataset collection.
 
 .. _trimAl: http://trimal.cgenomics.org