# HG changeset patch
# User greg
# Date 1501611985 14400
# Node ID f5ae6c86f75f737684676b6b5048f8e3f3c97988
# Parent  7000422fbaff8552c692e1b89db222e2dfe6bdf8
Uploaded

diff -r 7000422fbaff -r f5ae6c86f75f gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Thu Jun 08 12:51:58 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Tue Aug 01 14:26:25 2017 -0400
@@ -16,30 +16,30 @@
     #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
 #end if
 
-python $__tool_directory__/gene_family_phylogeny_builder.py
+python '$__tool_directory__/gene_family_phylogeny_builder.py'
 #if str($input_format) == 'ptalign':
     --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
-    --alignment_type 'aln'
-    --sequence_type 'protein'
+    --alignment_type aln
+    --sequence_type protein
 #else if str($input_format) == 'ptalignca':
     --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path'
-    --alignment_type 'aln'
+    --alignment_type aln
     --sequence_type $input_format_cond.sequence_type
 #else if str($input_format) == 'ptalignfiltered':
     --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path'
-    --alignment_type 'filter'
-    --sequence_type 'protein'
+    --alignment_type filter
+    --sequence_type protein
 #else if str($input_format) == 'ptalignfilteredca':
     --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path'
-    --alignment_type 'filter'
+    --alignment_type filter
     --sequence_type $input_format_cond.sequence_type
 #else if str($input_format) == 'ptaligntrimmed':
     --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path'
-    --alignment_type 'trim'
-    --sequence_type 'protein'
+    --alignment_type trim
+    --sequence_type protein
 #else if str($input_format) == 'ptaligntrimmedca':
     --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path'
-    --alignment_type 'trim'
+    --alignment_type trim
     --sequence_type $input_format_cond.sequence_type
 #end if
 --scaffold '$scaffold.fields.path'