Mercurial > repos > greg > phylogenomics_analysis

changeset 58:1b256588fb06 draft

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Uploaded
author greg
date Mon, 13 Feb 2017 09:33:37 -0500
parents c662ff5166df
children 963f84101cdc
files phylogenomics_analysis.xml
diffstat 1 files changed, 1 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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':