# 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'