Mercurial > repos > greg > phylogenomics_analysis
diff phylogenomics_analysis.xml @ 58:1b256588fb06 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 13 Feb 2017 09:33:37 -0500 |
| parents | c662ff5166df |
| children | 963f84101cdc |
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--- a/phylogenomics_analysis.xml Fri Feb 10 14:08:42 2017 -0500 +++ b/phylogenomics_analysis.xml Mon Feb 13 09:33:37 2017 -0500 @@ -19,9 +19,6 @@ #set input_format = $input_format_cond.input_format #set pipeline_output_dir = 'phylogenomicsAnalysis_dir' - #set scaffold_path = $scaffold.fields.path - #set scaffold_dir = $os.path.split($scaffold_path)[0] - #set scaffold_selection = $os.path.split($scaffold_path)[1] #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln') #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta') #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree') @@ -75,8 +72,7 @@ --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' --orthogroup_fna #end if - --scaffold_dir '$scaffold_dir' - --scaffold '$scaffold_selection' + --scaffold '$scaffold.fields.path' --method $method #if str($options_type.options_type_selector) == 'advanced':