# HG changeset patch
# User greg
# Date 1486990789 18000
# Node ID 913c3e0354cc7bac5add6757fedab7327463e92b
# Parent  37abc8473df137710f25035b7bc44f3813f2258a
Uploaded

diff -r 37abc8473df1 -r 913c3e0354cc assembly_post_processor.xml
--- a/assembly_post_processor.xml	Mon Feb 13 07:49:14 2017 -0500
+++ b/assembly_post_processor.xml	Mon Feb 13 07:59:49 2017 -0500
@@ -22,9 +22,8 @@
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-                    #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
                     --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
-                    --scaffold '$scaffold'
+                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                     --method '$options_type.target_gene_family_assembly_cond.method'
                 #end if
                 --gap_trimming $options_type.gap_trimming
@@ -136,7 +135,7 @@
  * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
  * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
  * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
- * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the Data Manager PlantTribes Scaffolds Downloader tool.
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data, installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
  * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
  * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
  * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.