# HG changeset patch
# User greg
# Date 1493404703 14400
# Node ID 23e20d346539c50ed3484bc952eaafcf5c15263c
# Parent  f3b6ddb952eb9857d47655ad73d9c9babcb5256f
Uploaded

diff -r f3b6ddb952eb -r 23e20d346539 gene_family_aligner.xml
--- a/gene_family_aligner.xml	Fri Apr 28 13:58:52 2017 -0400
+++ b/gene_family_aligner.xml	Fri Apr 28 14:38:23 2017 -0400
@@ -88,13 +88,13 @@
             </param>
             <when value="ptortho">
                 <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
                 <expand macro="cond_alignment_method" />
             </when>
             <when value="ptorthocs">
                 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
-                    <!-- <validator type="empty_files_path" /> -->
+                    <!-- <validator type="empty_extra_files_path" /> -->
                 </param>
                 <expand macro="cond_alignment_method" />
                 <expand macro="param_codon_alignments" />
@@ -123,7 +123,7 @@
         </data>
     </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>
         -->
@@ -156,9 +156,6 @@
  * **Alignment post-processing configuration** - select 'Yes' to enable multiple sequence alignment post-processing configuration options.
 
   - **Trimming method** - multiple sequence alignment trimming method.  PlantTribes trims alignments using two automated approaches implemented in trimAl.  Gap score based trimming removes alignments sites that do not achieve a user specified gap score.  For example, a setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment.  The automated heuristic trimming approach determines the best automated trimAl method to trim a given alignment as described in the trimAl tutorial `trimAl`_.
-
-.. _trimAl: http://trimal.cgenomics.org
-
     - **Nucleotide based**
 
       - **Gap score** - 1.0 - (the fraction of sequences with gap allowed in an alignment site).  The score is restricted to the range 0.0 - 1.0.  Zero value has no effect.
@@ -169,6 +166,8 @@
 
       - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences.  Zero value has no effect.
 
+.. _trimAl: http://trimal.cgenomics.org
+
     </help>
     <citations>
         <expand macro="citation1" />