# HG changeset patch
# User greg
# Date 1488384786 18000
# Node ID bbc153dbaee75afb3cca7c2beebb1bc25989e5de
# Parent  db3e35944c09c3e6f7f97de25648f6669f1482f2
Uploaded

diff -r db3e35944c09 -r bbc153dbaee7 kaks_analysis.xml
--- a/kaks_analysis.xml	Wed Mar 01 11:04:34 2017 -0500
+++ b/kaks_analysis.xml	Wed Mar 01 11:13:06 2017 -0500
@@ -25,7 +25,7 @@
             --coding_sequences_species_1 '$coding_sequences_species_1'
             --proteins_species_1 '$proteins_species_1'
             --comparison $comparison
-            #if str($comparison) == 'orthologs':
+            #if str($comparison_cond.comparison) == 'orthologs':
                 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
                 --proteins_species_2 '$comparison_cond.proteins_species_2'
             #end if
@@ -51,7 +51,7 @@
             <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>
         <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
-        <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (FNA) sequences fasta file for the species" />
+        <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
         <conditional name="comparison_cond">
             <param name="comparison" type="select" label="Select method for pairwise sequence comparison to determine homolgous pairs" help="Cross species comparison requires selection of inputs for second species">
                 <option value="paralogs" selected="true">Self species comparison</option>
@@ -60,7 +60,7 @@
             <when value="paralogs" />
             <when value="orthologs">
                 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" />
-                <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (FNA) sequences fasta file for the second species" />
+                <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
             </when>
         </conditional>
         <conditional name="options_type">