# HG changeset patch
# User greg
# Date 1483639411 18000
# Node ID cb7487bdab99854eeb81c852e213b01e4a315ccc
# Parent  1cf39b1af2488a24df733169003d348874d1ce65
Uploaded

diff -r 1cf39b1af248 -r cb7487bdab99 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Jan 05 08:00:33 2017 -0500
+++ b/gene_family_classifier.xml	Thu Jan 05 13:03:31 2017 -0500
@@ -17,6 +17,10 @@
                 #set create_ortho_sequences = True
                 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                 #set dest_dir = $output.extra_files_path
+                #set create_orthogroup_cond = $options_type.create_orthogroup_cond
+                #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
+                #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
+                #set create_corresponding_coding_sequences = $create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences
                 mkdir -p $dest_dir &&
             #else:
                 #set create_ortho_sequences = False
@@ -32,9 +36,11 @@
                     --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa
                     --taxa_present $options_type.single_copy_cond.taxa_present
                 #end if
-                #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                #if str($create_orthogroup) == 'yes':
                     --orthogroup_fasta
-                    --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
+                    #if $create_corresponding_coding_sequences == 'yes':
+                        --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences"
+                    #end if
                 #end if
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
@@ -113,7 +119,16 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="coding_sequences" format="fasta" type="data" label="Corresponding coding sequences (CDS) fasta file"/>
+                        <conditional name="create_corresponding_coding_sequences_cond">
+                            <param name="create_corresponding_coding_sequences" type="select" label="Create corresponding coding sequences?">
+                                <option value="no" selected="true">No</option>
+                                <option value="yes">Yes</option>
+                            </param>
+                            <when value="no" />
+                            <when value="yes">
+                                <param name="coding_sequences" format="fasta" type="data" label="Corresponding coding sequences (CDS) fasta file"/>
+                            </when>
+                        </conditional>
                     </when>
                 </conditional>
             </when>