# HG changeset patch
# User greg
# Date 1486740138 18000
# Node ID c24ca7fed70c6919b3cbe3e8b643d196bc3b037b
# Parent  ebc846754dcbfd305debf9ee41a589b29b0b91d6
Uploaded

diff -r ebc846754dcb -r c24ca7fed70c phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Fri Feb 10 09:28:28 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Feb 10 10:22:18 2017 -0500
@@ -122,6 +122,7 @@
                     #end if
                 #end if
             #end if
+            >/dev/null
 
             && echo "Sequence alignments and corresponding phylogenies"
             #if str($input_format) == 'ptortho':
@@ -149,8 +150,8 @@
     <inputs>
         <conditional name="input_format_cond">
             <param name="input_format" type="select" label="Select type of data to sub sample">
-                <option value="ptortho">Gene family clusters</option>
-                <option value="ptorthocs">Gene family clusters and corresponding coding sequences</option>
+                <option value="ptortho">Precomputed orthologous gene family clusters</option>
+                <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
             </param>
             <when value="ptortho">
                 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
@@ -291,7 +292,7 @@
         <data name="output_aln" format="txt" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
         </data>
-        <data name="output_tree" format="ptpt" label="Phylogenetic trees on ${on_string}">
+        <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
         </data>
     </outputs>