# HG changeset patch
# User greg
# Date 1483642897 18000
# Node ID b14a129fe55f7cf99462704dec258cfc447736ca
# Parent  cb7487bdab99854eeb81c852e213b01e4a315ccc
Uploaded

diff -r cb7487bdab99 -r b14a129fe55f gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Jan 05 13:03:31 2017 -0500
+++ b/gene_family_classifier.xml	Thu Jan 05 14:01:37 2017 -0500
@@ -20,7 +20,11 @@
                 #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 = $create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences
+                #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
+                    #set create_corresponding_coding_sequences = True
+                #else:
+                    #set create_corresponding_coding_sequences = False
+                #endif
                 mkdir -p $dest_dir &&
             #else:
                 #set create_ortho_sequences = False
@@ -38,7 +42,7 @@
                 #end if
                 #if str($create_orthogroup) == 'yes':
                     --orthogroup_fasta
-                    #if $create_corresponding_coding_sequences == 'yes':
+                    #if $create_corresponding_coding_sequences:
                         --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences"
                     #end if
                 #end if
@@ -53,7 +57,11 @@
                 #end if
             #end if
             #if $create_ortho_sequences:
-                && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                #if $create_corresponding_coding_sequences:
+                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                #else:
+                    && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
+                #end if
                 && ls $orthogroups_fasta_src_dir >> $output
                 && mv $orthogroups_fasta_src_dir/* $dest_dir
             #end if