# HG changeset patch
# User greg
# Date 1486051384 18000
# Node ID 36f85b2570be3069e3ee111815378acac093a726
# Parent  d485da50616bf23b1eed0b4a5acedc1a8dc67655
Uploaded

diff -r d485da50616b -r 36f85b2570be gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 02 10:10:43 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 02 11:03:04 2017 -0500
@@ -33,9 +33,9 @@
                     #set create_ortho_sequences = True
                     #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                     #if $create_corresponding_coding_sequences:
-                    	#set dest_dir = $output_pgfccs.extra_files_path
+                    	#set dest_dir = $output_ptefccs.extra_files_path
                     #else:
-                    	#set dest_dir = $output_pgfc.extra_files_path
+                    	#set dest_dir = $output_ptefc.extra_files_path
                   	#end if
                     mkdir -p $dest_dir &&
                 #else:
@@ -79,11 +79,11 @@
 
             #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_pgfccs
-                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfccs
+                    && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptefccs
+                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptefccs
                 #else:
-                    && 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
+                    && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptefc
+                    && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptefc
                 #end if
                 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
             #end if
@@ -169,10 +169,10 @@
         <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_pgfc" format="pgfc" label="Gene family clusters on ${on_string}">
+        <data name="output_ptefc" format="ptefc" 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_pgfccs" format="pgfccs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
+        <data name="output_ptefccs" format="ptefccs" 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">