# HG changeset patch
# User greg
# Date 1488466983 18000
# Node ID 01278db07d6f89ce20c099d55c39c7b26cf3581e
# Parent  4e23c98465e9e0a2ec7c442cbaa8cb6f061b6272
Uploaded

diff -r 4e23c98465e9 -r 01278db07d6f kaks_analysis.xml
--- a/kaks_analysis.xml	Thu Mar 02 09:45:04 2017 -0500
+++ b/kaks_analysis.xml	Thu Mar 02 10:03:03 2017 -0500
@@ -76,8 +76,8 @@
         ]]>
     </command>
     <inputs>
-        <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 (proteins) sequences fasta file for the species" />
+        <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species1" />
+        <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species1" />
         <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>
@@ -85,8 +85,8 @@
             </param>
             <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 (proteins) sequences fasta file for the second species" />
+                <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species2" />
+                <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">
@@ -144,6 +144,7 @@
                 </conditional>
             </when>
         </conditional>
+        <!-- Required due to the Emmix license -->
         <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
             <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
         </param>
@@ -185,14 +186,14 @@
 
 **Options**
 
- * **Required options**
+ * **Required**
 
-  - **Coding sequences (CDS) fasta file for the species** - Coding sequences (CDS) fasta file for the first species.
-  - **Aamino acids (proteins) sequences fasta file for the species** - Aamino acids (proteins) sequences fasta file for the first species
-  - **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 second species).
+  - **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.
 
- * **Other (optional) options**
+ * **Optional**
 
   - **Minimum sequence pairwise coverage length between homologous pairs** - Minimum sequence pairwise coverage length between homologous pairs (e.g., 0.5 results in 50% coverage.  Legal values lie between 0.3 and 1.0.
   - **Evolutionary rate for recalibrating synonymous subsitutions (ks) of species** - (applies to paralogous ks analysis) Recalibrate synonymous subsitutions (ks) of species using a predetermined evoutionary rate that can be determined from a species tree inferred from a collection single copy genes from taxa of interest (Cui et al., 2006).