# HG changeset patch
# User greg
# Date 1494524544 14400
# Node ID ab4e77327a0539cc3d0c9892ee2f7f034dcd078a
# Parent  f33369f4392ad69b960daa341843e96abd4f28f5
Uploaded

diff -r f33369f4392a -r ab4e77327a05 gene_family_phylogeny_builder.xml
--- a/gene_family_phylogeny_builder.xml	Wed May 10 14:29:26 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Thu May 11 13:42:24 2017 -0400
@@ -54,14 +54,14 @@
                     ## 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 '$output_tree.files_path'
+            ##--output_tree '$output_tree'
+            ##--output_tree_dir '$output_tree.files_path'
         ]]>
     </command>
     <inputs>
@@ -134,10 +134,18 @@
         <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum orthogroup size" />
     </inputs>
     <outputs>
+        <!--
         <data name="output_phylip" format="ptphylip" label="Gene family orthogroup phylip multiple sequence alignments on ${on_string}">
             <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
         </data>
         <data name="output_tree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
+        -->
+        <collection name="phylip" type="list">
+            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" visible="true" ext="fasta" />
+        </collection>
+        <collection name="tree" type="list">
+            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" visible="true" ext="fasta" />
+        </collection>
     </outputs>
     <tests>
         <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.