# HG changeset patch
# User greg
# Date 1483644398 18000
# Node ID 505c38cafb9c7f31e73bb5e562a697e3c365555e
# Parent  21298684d201addc521e1e97d4ba659975bc75fc
Uploaded

diff -r 21298684d201 -r 505c38cafb9c phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 05 10:32:14 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 14:26:38 2017 -0500
@@ -17,7 +17,7 @@
             #set dest_dir = $output.extra_files_path
             mkdir -p $dest_dir &&
             PhylogenomicsAnalysis
-            --orthogroup_faa "$orthogroup_fna.extra_files_path"
+            --orthogroup_faa "$orthogroup_faa.extra_files_path"
             --scaffold "$scaffold"
             --method $method
             #if str($options_type.options_type_selector) == 'advanced':
@@ -26,6 +26,8 @@
                     #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
                     #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
                     #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
+                    #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
+                    #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
                     #if str($multiple_sequence_alignments_option) == 'create_alignments':
                         --create_alignments
                     #else if str($multiple_sequence_alignments_option) == 'add_alignments':
@@ -36,7 +38,9 @@
                     #end if
                     #if str($multiple_codon_alignments) == 'yes':
                         --codon_alignments
-                        --orthogroup_fna "$orthogroup_fna"
+                        #if str($use_corresponding_coding_sequences) == 'yes':
+                            --orthogroup_fna
+                        #end if
                         --sequence_type $multiple_codon_alignments_cond.sequence_type
                     #end if
                 #end if
@@ -73,7 +77,7 @@
         ]]>
     </command>
     <inputs>
-        <param name="orthogroup_fna" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
+        <param name="orthogroup_faa" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
@@ -119,6 +123,18 @@
                                     <option value="protein" selected="true">Amino acid based</option>
                                     <option value="dna">Nucleotide based</option>
                                 </param>
+
+
+                                <conditional name="use_corresponding_coding_sequences_cond">
+                                    <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool">
+                                        <option value="no" selected="true">No</option>
+                                        <option value="yes">Yes</option>
+                                    </param>
+                                    <when value="no" />
+                                    <when value="yes" />
+                                </conditional>
+
+
                             </when>
                             <when value="no"/>
                         </conditional>