Mercurial > repos > greg > gene_family_classifier
changeset 37:36f85b2570be draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 02 Feb 2017 11:03:04 -0500 |
| parents | d485da50616b |
| children | b63f96ff6708 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- 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">