# HG changeset patch
# User greg
# Date 1494596356 14400
# Node ID e6f16430822d0854b0edec0bbc4375afa5f46c0a
# Parent  61825c063bf3f1f5051a99ea5e4f9e2225a7a63e
Uploaded

diff -r 61825c063bf3 -r e6f16430822d gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Fri May 12 09:39:06 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Fri May 12 09:39:16 2017 -0400
@@ -54,14 +54,12 @@
                     ## configuration will be used if the --rooting_order flag is missing.
                 #end if
                 --bootstrap_replicates $bootstrap_replicates
-                ##--output_phylip '$output_phylip'
-                ##--output_phylip_dir '$output_phylip.files_path'
+                --output_phylip '$output_phylip'
+                --output_phylip_dir '$output_phylip.files_path'
             #end if
             --min_orthogroup_size $min_orthogroup_size
             --max_orthogroup_size $max_orthogroup_size
             --num_threads \${GALAXY_SLOTS:-4}
-            ##--output_tree '$output_tree'
-            ##--output_tree_dir '$output_tree.files_path'
         ]]>
     </command>
     <inputs>
@@ -134,10 +132,10 @@
         <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" />
     </inputs>
     <outputs>
-        <collection name="phylip" type="list">
-            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
-        </collection>
-        <collection name="tree" type="list">
+        <data name="output_phylip" format="ptphylip" label="Orthogroup phylip multiple sequence alignments on ${on_string}">
+            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
+        </data>
+        <collection name="tree" type="list" label="GeneFamilyPhylogenyBuilder phylogenetic trees on ${on_string}">
             <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
         </collection>
     </outputs>