# HG changeset patch
# User greg
# Date 1486064494 18000
# Node ID b63f96ff6708fcd7d0d9f3139d13a31e7472cf69
# Parent 36f85b2570be3069e3ee111815378acac093a726
Uploaded
diff -r 36f85b2570be -r b63f96ff6708 gene_family_classifier.xml
--- a/gene_family_classifier.xml Thu Feb 02 11:03:04 2017 -0500
+++ b/gene_family_classifier.xml Thu Feb 02 14:41:34 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_ptefccs.extra_files_path
+ #set dest_dir = $output_ptcgfcs.extra_files_path
#else:
- #set dest_dir = $output_ptefc.extra_files_path
+ #set dest_dir = $output_ptcgf.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_ptefccs
- && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptefccs
+ && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgfcs
+ && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgfcs
#else:
- && 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
+ && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptcgf
+ && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptcgf
#end if
&& mv $orthogroups_fasta_src_dir/* $dest_dir || true
#end if
@@ -169,10 +169,10 @@
save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'
-
+
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'
-
+
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'