# HG changeset patch
# User greg
# Date 1488568569 18000
# Node ID 887a918134da56969593b42ea4ae31082b1db47b
# Parent  e188f52adf1d733fe79207723b393cac509a0577
Uploaded

diff -r e188f52adf1d -r 887a918134da kaks_analysis.xml
--- a/kaks_analysis.xml	Thu Mar 02 10:48:29 2017 -0500
+++ b/kaks_analysis.xml	Fri Mar 03 14:16:09 2017 -0500
@@ -35,7 +35,6 @@
                 #set set_upper_ks_limit = 'no'
             #end if
             KaKsAnalysis
-            --config_dir '$scaffold.fields.path'
             --num_threads \${GALAXY_SLOTS:-4}
             --coding_sequences_species_1 '$coding_sequences_species_1'
             --proteins_species_1 '$proteins_species_1'
@@ -99,10 +98,6 @@
                 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species2" />
             </when>
         </conditional>
-        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
-            <options from_data_table="plant_tribes_scaffolds" />
-            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
-        </param>
         <conditional name="options_type">
             <param name="options_type_selector" type="select" label="Options Configuration">
                 <option value="basic" selected="true">Basic</option>
@@ -147,7 +142,7 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" />
+                        <param name="num_of_components" type="integer" value="0" min="0" label="Number of components to fit to synonymous subsitutions (ks) distribution" />
                     </when>
                 </conditional>
                 <conditional name="set_lower_ks_limit_cond">
@@ -219,7 +214,6 @@
   - **Coding sequences (CDS) fasta file for species1** - Coding sequences (CDS) fasta file for species1.
   - **Aamino acids (proteins) sequences fasta file for species1** - Aamino acids (proteins) sequences fasta file for species1
   - **Select method for pairwise sequence comparison to determine homolgous pairs** - Pairwise sequence comparison to determine homolgous pairs (cross species comparison requires selection of inputs for species2).
-  - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
 
  * **Optional**