# HG changeset patch
# User greg
# Date 1486584025 18000
# Node ID 921804e9ec8c880c82b5451840d2254137a5a093
# Parent  3b2d35b7526814fb4ca95fb2dd9c86ce355a26f4
Uploaded

diff -r 3b2d35b75268 -r 921804e9ec8c gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Feb 08 14:25:16 2017 -0500
+++ b/gene_family_classifier.xml	Wed Feb 08 15:00:25 2017 -0500
@@ -33,18 +33,6 @@
                     #set specify_super_orthos = False
                 #end if
 
-                #if str($specify_single_copy) == 'yes':
-                    #set single_copy_orthogroup = True
-                    #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
-                    #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
-                    #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
-                    ## FixMe: the single_copy_custom option is not currently supported.
-                    #set single_copy = $single_copy_cond.single_copy
-                    mkdir -p $single_copy_fasta_dest_dir &&
-                #else:
-                    #set single_copy_orthogroup = False
-                #end if
-
                 #if str($create_orthogroup) == 'yes':
                     #set create_ortho_sequences = True
                     #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
@@ -62,6 +50,21 @@
                     #set create_ortho_sequences = False
                     #set create_corresponding_coding_sequences = False
                 #end if
+
+                #if str($specify_single_copy) == 'yes':
+                    #set single_copy_orthogroup = True
+                    #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
+                    ## FixMe: the single_copy_custom option is not currently supported.
+                    #set single_copy = $single_copy_cond.single_copy
+                    #if $create_ortho_sequences:
+                        #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
+                        #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
+                        mkdir -p $single_copy_fasta_dest_dir &&
+                    #end if:
+                #else:
+                    #set single_copy_orthogroup = False
+                #end if
+
             #else:
                 #set single_copy_orthogroup = False
                 #set create_ortho_sequences = False
@@ -101,21 +104,21 @@
                 #end if
             #end if
 
-            #if $create_ortho_sequences:
+            #if $create_ortho_sequences and $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0:
                 #if $create_corresponding_coding_sequences:
                     && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
                 #else:
                     && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
                 #end if
-                #if $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0:
-                    && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
-                #end if
+                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
             #end if
 
             #if $single_copy_orthogroup:
-                && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
-                #if $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0:
+                #if $create_ortho_sequences and $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0:
+                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
                     && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
+                #else:
+                    && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
                 #end if
             #end if
         ]]>
@@ -230,7 +233,10 @@
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
         </data>
         <data name="output_ptsco" format="txt" label="Single copy orthogroup on ${on_string}">
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
+            <filter>options_type['options_type_selector'] == 'advanced' and and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
+        </data>
+        <data name="output_single_copy" format="tabular" label="Single copy orthogroup on ${on_string}">
+            <filter>options_type['options_type_selector'] == 'advanced' and and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
         </data>
         <collection name="orthos" type="list">
             <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />