--- a/gene_family_aligner.py	Mon Apr 10 14:46:51 2017 -0400
+++ b/gene_family_aligner.py	Tue Apr 11 14:21:35 2017 -0400
@@ -11,15 +11,15 @@
 parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
 parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach")
 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('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of')
+parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='"Maximum number of iterations')
 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 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('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
 
 args = parser.parse_args()
 
@@ -37,11 +37,11 @@
     cmd += ' --codon_alignments'
 if args.automated_trimming is not None:
     cmd += ' --automated_trimming'
-if args.gap_trimming is not None:
+if args.gap_trimming > 0:
     cmd += ' --gap_trimming %4f' % args.gap_trimming
-if args.remove_sequences is not None:
+if args.remove_sequences > 0:
     cmd += ' --remove_sequences %4f' % args.remove_sequences
-if args.iterative_realignment is not None:
+if args.iterative_realignment > 0:
     cmd += ' --iterative_realignment %d' % args.iterative_realignment
 # Run the command.
 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)

--- 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>

--- a/macros.xml	Mon Apr 10 14:46:51 2017 -0400
+++ b/macros.xml	Tue Apr 11 14:21:35 2017 -0400
@@ -70,6 +70,12 @@
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
         </param>
     </xml>
+    <xml name="param_sequence_type">
+        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
+            <option value="protein" selected="true">Amino acid based</option>
+            <option value="dna">Nucleotide based</option>
+        </param>
+    </xml>
     <xml name="cond_alignment_method">
         <conditional name="alignment_method_cond">
             <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
@@ -96,7 +102,7 @@
                         <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
                     </param>
                     <when value="gap_trimming">
-                        <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
                     </when>
                     <when value="automated_trimming" />
                 </conditional>
@@ -107,8 +113,8 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
-                        <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
                     </when>
                 </conditional>
             </when>