# HG changeset patch
# User greg
# Date 1486989602 18000
# Node ID 1e639e679f61996160839bbc46198b84cdca3117
# Parent  ff5c714e01d18f96c53bae72398661f6781fe726
Uploaded

diff -r ff5c714e01d1 -r 1e639e679f61 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Wed Feb 08 09:13:53 2017 -0500
+++ b/assembly_post_processor.xml	Mon Feb 13 07:40:02 2017 -0500
@@ -22,11 +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_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
-                    #set scaffold_dir = $os.path.split($scaffold_path)[0]
-                    #set scaffold = $os.path.split($scaffold_path)[1]
+                    #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
                     --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
-                    --scaffold_dir '$scaffold_dir'
                     --scaffold '$scaffold'
                     --method '$options_type.target_gene_family_assembly_cond.method'
                 #end if
@@ -105,7 +102,7 @@
             <output_collection name="transcripts" type="list">
                 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
                 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
-                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
                 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
             </output_collection>
         </test>
@@ -117,12 +114,12 @@
             <param name="dereplicate" value="yes" />
             <param name="min_length" value="200" />
             <output_collection name="transcripts" type="list">
-                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
-                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/>
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
             </output_collection>
         </test>
     </tests>
@@ -139,7 +136,7 @@
  * **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.
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the [Data Manager PlantTribes Scaffolds Downloader tool](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/4c96b684f0fd).
  * **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.