# HG changeset patch
# User greg
# Date 1493401737 14400
# Node ID c03437a39e081d4e5ce36bfe320e09ce790648e2
# Parent  0e55cec5ec6bcc3415947f00f999c1fc49b58f3d
Uploaded

diff -r 0e55cec5ec6b -r c03437a39e08 gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Fri Apr 28 09:43:53 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Fri Apr 28 13:48:57 2017 -0400
@@ -75,34 +75,34 @@
             </param>
             <when value="ptalign">
                 <param name="input_ptalign" format="ptalign" type="data" label="Proteins orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
             </when>
             <when value="ptalignca">
                 <param name="input_ptalignca" format="ptalignca" type="data" label="Protein and coding sequences orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
                 <expand macro="param_sequence_type" />
             </when>
             <when value="ptalignfiltered">
                 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered proteins orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
             </when>
             <when value="ptalignfilteredca">
                 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered protein and coding sequences orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
                 <expand macro="param_sequence_type" />
             </when>
             <when value="ptaligntrimmed">
                 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed proteins orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
             </when>
             <when value="ptaligntrimmedca">
                 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed protein and coding sequences orthogroup alignments">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
                 <expand macro="param_sequence_type" />
             </when>
@@ -116,7 +116,7 @@
             </param>
             <when value="raxml">
                 <conditional name="rooting_order_file_cond">
-                    <param name="rooting_order_file" type="select" label="Rooting order configuration?">
+                    <param name="rooting_order_file" type="select" label="Rooting order configuration">
                         <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
@@ -136,7 +136,7 @@
         <data name="output_pttree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
     </outputs>
     <tests>
-        <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
+        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
         <test>
         </test>
         -->
@@ -157,9 +157,9 @@
 
 **Other options**
 
- * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML.  Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub repository `planttribes`_.  Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
+ * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML.  Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_.  Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
 
-.. _planttribes: https://github.com/dePamphillis/PlantTribes/config
+.. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config
 
  * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100).
  * **Maximum orthogroup size** - Maximum number of sequences allowed in orthogroup alignments (default = 100).