Mercurial > repos > greg > gene_family_classifier
changeset 34:9a60634252fd draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 01 Feb 2017 15:01:19 -0500 |
| parents | c1a3b77de0f0 |
| children | 0fc60c5cb719 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 11 insertions(+), 6 deletions(-) [+] |
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--- 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">