Mercurial > repos > greg > gene_family_classifier
changeset 18:b14a129fe55f draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 05 Jan 2017 14:01:37 -0500 |
| parents | cb7487bdab99 |
| children | c4a9c23334a4 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/gene_family_classifier.xml Thu Jan 05 13:03:31 2017 -0500 +++ b/gene_family_classifier.xml Thu Jan 05 14:01:37 2017 -0500 @@ -20,7 +20,11 @@ #set create_orthogroup_cond = $options_type.create_orthogroup_cond #set create_orthogroup = $create_orthogroup_cond.create_orthogroup #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond - #set create_corresponding_coding_sequences = $create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences + #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': + #set create_corresponding_coding_sequences = True + #else: + #set create_corresponding_coding_sequences = False + #endif mkdir -p $dest_dir && #else: #set create_ortho_sequences = False @@ -38,7 +42,7 @@ #end if #if str($create_orthogroup) == 'yes': --orthogroup_fasta - #if $create_corresponding_coding_sequences == 'yes': + #if $create_corresponding_coding_sequences: --coding_sequences "$create_corresponding_coding_sequences_cond.coding_sequences" #end if #end if @@ -53,7 +57,11 @@ #end if #end if #if $create_ortho_sequences: - && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output + #if $create_corresponding_coding_sequences: + && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output + #else: + && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output + #end if && ls $orthogroups_fasta_src_dir >> $output && mv $orthogroups_fasta_src_dir/* $dest_dir #end if