# HG changeset patch
# User greg
# Date 1485979279 18000
# Node ID 9a60634252fdbb0365aaeabe947ecd6aee78ebae
# Parent  c1a3b77de0f043c9e29c148c589f44e3b1977c01
Uploaded

diff -r c1a3b77de0f0 -r 9a60634252fd gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Feb 01 14:50:48 2017 -0500
+++ b/gene_family_classifier.xml	Wed Feb 01 15:01:19 2017 -0500
@@ -28,7 +28,11 @@
                     #import os
                     #set create_ortho_sequences = True
                     #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
-                    #set dest_dir = $output.extra_files_path
+                    #if $create_corresponding_coding_sequences:
+                    	#set dest_dir = $output_pgfccs.extra_files_path
+                    #else:
+                    	#set dest_dir = $output_pgfc.extra_files_path
+                  	#end if
                     mkdir -p $dest_dir &&
                 #else:
                     #set create_ortho_sequences = False
@@ -71,11 +75,12 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
+                    && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfccs
+                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfccs
                 #else:
-                    && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
+                    && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfc
+                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfc
                 #end if
-                && ls -al $orthogroups_fasta_src_dir | grep f >> $output
                 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
             #end if
 
@@ -160,10 +165,10 @@
         <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
             <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
         </data>
-        <data name="output" format="pgfc" label="Gene family clusters on ${on_string}">
+        <data name="output_pgfc" format="pgfc" label="Gene family clusters on ${on_string}">
             <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'] == 'no'</filter>
         </data>
-        <data name="output" format="pgfccs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
+        <data name="output_pgfccs" format="pgfccs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
             <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>
         <collection name="orthos" type="list">