Mercurial > repos > greg > phylogenomics_analysis

changeset 44:3592048fb258 draft

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Uploaded
author greg
date Fri, 03 Feb 2017 13:46:21 -0500
parents 923a54b9425c
children c27c13bb4615
files phylogenomics_analysis.xml
diffstat 1 files changed, 2 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/phylogenomics_analysis.xml	Fri Feb 03 13:41:08 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Feb 03 13:46:21 2017 -0500
@@ -23,14 +23,13 @@
             #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'
+            #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
 
             #if str($input_format) == 'ptcgf':
                 #set dest_fasta_dir = $output_fasta_ptcgf.extra_files_path
                 #set multiple_codon_alignments = 'no'
                 #set use_corresponding_coding_sequences = 'no
             #else:
-                ## str($input_format) == 'ptcgfcs':
                 #set dest_fasta_dir = $output_fasta_ptcgfcs.extra_files_path
                 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
                 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
@@ -65,7 +64,7 @@
             #end if
 
             PhylogenomicsAnalysis
-            --num_threads '\${GALAXY_SLOTS:-4}'
+            --num_threads \${GALAXY_SLOTS:-4}
             --orthogroup_faa '$input.extra_files_path'
             --scaffold_dir '$scaffold_dir'
             --scaffold '$scaffold_selection'