# HG changeset patch
# User greg
# Date 1486753216 18000
# Node ID ae197e9e9497d34ffadc5a6b7a3cebf500079e3f
# Parent  150087c2f41d574dbb1effed0e7c0fca8cd7c0d0
Uploaded

diff -r 150087c2f41d -r ae197e9e9497 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Fri Feb 10 14:00:08 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Feb 10 14:00:16 2017 -0500
@@ -101,6 +101,9 @@
                         #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                         #if str($rooting_order_file) == 'yes':
                             --rooting_order '$rooting_order_file_cond.rooting_order'
+                        #else:
+                            #set default_rooting_order = $__tool_directory__/rooting_order.config
+                            --rooting_order '$default_rooting_order'
                         #end if
                         --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
                     #end if
@@ -233,13 +236,13 @@
                             </param>
                             <when value="raxml">
                                 <conditional name="rooting_order_file_cond">
-                                    <param name="rooting_order_file" type="select" label="Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?">
+                                    <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select no for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
                                         <option value="no" selected="true">No</option>
                                         <option value="yes">Yes</option>
                                     </param>
                                     <when value="no" />
                                     <when value="yes">
-                                        <param name="rooting_order" format="txt" type="data" label="History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees" />
+                                        <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
                                     </when>
                                 </conditional>
                                 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
@@ -326,8 +329,7 @@
         * **Phylogenetic trees options**
 
         - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
-        - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
-        - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** - History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
+        - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
         - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
         - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
         - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.