Mercurial > repos > greg > gene_family_classifier
changeset 97:484bedd86474 draft
Uploaded
author | greg |
---|---|
date | Mon, 27 Feb 2017 10:48:07 -0500 |
parents | ba924b724a8d |
children | e53492ae4ac0 |
files | gene_family_classifier.xml |
diffstat | 1 files changed, 7 insertions(+), 34 deletions(-) [+] |
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line diff
--- a/gene_family_classifier.xml Mon Feb 27 10:48:00 2017 -0500 +++ b/gene_family_classifier.xml Mon Feb 27 10:48:07 2017 -0500 @@ -22,45 +22,31 @@ #set create_orthogroup = $create_orthogroup_cond.create_orthogroup #set specify_single_copy_cond = $options_type.specify_single_copy_cond #set specify_single_copy = $specify_single_copy_cond.specify_single_copy - #if str($specify_super_orthogroups) == 'yes': #set specify_super_orthos = True #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups #else: #set specify_super_orthos = False #end if - #if str($create_orthogroup) == 'yes': #set create_ortho_sequences = True - #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond - #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': #set create_corresponding_coding_sequences = True - #set orthogroups_fasta_dest_dir = $output_ptorthocs.files_path #else: #set create_corresponding_coding_sequences = False - #set orthogroups_fasta_dest_dir = $output_ptortho.files_path #end if - mkdir -p $orthogroups_fasta_dest_dir && #else: #set create_ortho_sequences = False #set create_corresponding_coding_sequences = False #end if - #if str($specify_single_copy) == 'yes': #set single_copy_orthogroup = True #set single_copy_cond = $specify_single_copy_cond.single_copy_cond #set single_copy = $single_copy_cond.single_copy - #if $create_ortho_sequences: - #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') - #set single_copy_fasta_dest_dir = $output_ptsco.files_path - mkdir -p $single_copy_fasta_dest_dir && - #end if: #else: #set single_copy_orthogroup = False #end if - #else: #set single_copy_orthogroup = False #set create_ortho_sequences = False @@ -100,34 +86,21 @@ #end if #end if #end if - >/dev/null - #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': - #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': - && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log - #else: - && rm geneFamilyClassification_dir/hmmscan.log - #end if + #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both' and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': + --save_hmmscan_log + --hmmscan_log '$hmmscan_log' #end if - #if $create_ortho_sequences: #if $create_corresponding_coding_sequences: - #set out_file = $output_ptorthocs + --output_ptorthocs '$output_ptorthocs' #else: - #set out_file = $output_ptortho + --output_ptortho '$output_ptortho' #end if - && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true - && echo -e "<html>\n<head>\n<title>orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $out_file - && for f in "$orthogroups_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $out_file; fi; done - && echo -e "</ul>\n</body>\n</html>\n" >> $out_file #end if - #if $single_copy_orthogroup: #if $create_ortho_sequences: - && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true - && echo -e "<html>\n<head>\n<title>single copy orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $output_ptsco - && for f in "$single_copy_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $output_ptsco; fi; done - && echo -e "</ul>\n</body>\n</html>\n" >> $output_ptsco + --output_ptsco '$output_ptsco' #end if #end if ]]> @@ -177,7 +150,7 @@ </param> <when value="no"/> <when value="yes"> - <param name="super_orthogroups" type="select" label="Super Orthogroups"> + <param name="super_orthogroups" type="select" label="Super orthogroups clustering specification"> <option value="min_evalue" selected="true">Minimum e-value</option> <option value="avg_evalue">Average e-value</option> </param>