# HG changeset patch
# User greg
# Date 1486147581 18000
# Node ID 3592048fb25881cb578bf9a1b88ba9e9d1dc235f
# Parent  923a54b9425c0c958e6d095459c70449c7779f85
Uploaded

diff -r 923a54b9425c -r 3592048fb258 phylogenomics_analysis.xml
--- 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'