--- a/gene_family_aligner.xml	Mon Apr 10 14:46:51 2017 -0400
+++ b/gene_family_aligner.xml	Tue Apr 11 14:21:35 2017 -0400
@@ -38,7 +38,7 @@
             #if str($remove_gappy_sequences) == 'yes':
                 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
                 #set trim_type = $trim_type_cond.trim_type
-                #if str($trim_type) == 'gap_trimming':
+                #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
                     --gap_trimming $trim_type_cond.gap_trimming
                 #else:
                     ## str($trim_type) == 'automated_trimming'
@@ -47,8 +47,12 @@
                 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
                 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
                 #if str($remove_sequences_with_gaps) == 'yes':
-                    --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
-                    --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
+                    #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
+                        --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
+                    #end if
+                    #if str($remove_sequences_with_gaps_cond.iterative_realignment):
+                        --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
+                    #end if
                     #if $output_codon_alignments:
                         --output '$output_aln_filtered_ca'
                         --output_dir '$output_aln_filtered_ca.files_path'
@@ -83,11 +87,15 @@
                 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
             </param>
             <when value="ptortho">
-                <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
+                <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters">
+                    <validator type="empty_files_path" />
+                </param>
                 <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" />
+                <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences">
+                    <validator type="empty_files_path" />
+                </param>
                 <expand macro="cond_alignment_method" />
                 <expand macro="param_codon_alignments" />
             </when>