Mercurial > repos > greg > gene_family_classifier
changeset 47:4a6834056e1e draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 07 Feb 2017 14:24:32 -0500 |
| parents | 6c3fa9907d9c |
| children | 906d5277042c |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/gene_family_classifier.xml Tue Feb 07 13:53:56 2017 -0500 +++ b/gene_family_classifier.xml Tue Feb 07 14:24:32 2017 -0500 @@ -25,7 +25,7 @@ #set specify_single_copy = $specify_single_copy_cond.specify_single_copy #if str($specify_single_copy) == 'yes': - #set specify_single_copy = True + #set single_copy_orthogroup = True #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path #set single_copy_cond = $specify_single_copy_cond.single_copy_cond @@ -33,7 +33,7 @@ #set single_copy = $single_copy_cond.single_copy mkdir -p $single_copy_fasta_dest_dir && #else: - #set specify_single_copy = False + #set single_copy_orthogroup = False #end if #if str($create_orthogroup) == 'yes': @@ -54,7 +54,7 @@ #set create_corresponding_coding_sequences = False #end if #else: - #set specify_single_copy = False + #set single_copy_orthogroup = False #set create_ortho_sequences = False #set create_corresponding_coding_sequences = False #end if @@ -69,7 +69,7 @@ #if str($options_type.options_type_selector) == 'advanced': --super_orthogroups $options_type.super_orthogroups - #if $specify_single_copy: + #if $single_copy_orthogroup: --single_copy_taxa $single_copy_cond.single_copy_taxa --taxa_present $single_copy_cond.taxa_present #end if @@ -99,7 +99,7 @@ && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true #end if - #if $specify_single_copy: + #if $single_copy_orthogroup: && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true #end if