# HG changeset patch
# User greg
# Date 1508945426 14400
# Node ID 2fc444a858b6ff7408a1b292b4be0c16436e9aaf
# Parent  a22dd6959e5a6e38a0885e6b0564f843872de150
Uploaded

diff -r a22dd6959e5a -r 2fc444a858b6 gene_family_integrator.xml
--- a/gene_family_integrator.xml	Mon Oct 09 08:57:59 2017 -0400
+++ b/gene_family_integrator.xml	Wed Oct 25 11:30:26 2017 -0400
@@ -18,6 +18,7 @@
 --orthogroup_fasta '$input_dir'
 --scaffold '$scaffold.fields.path'
 --method $method
+&>proc.log
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data_collection" collection_type="list" label="Classified orthogroup fasta files" />
@@ -30,10 +31,28 @@
         </collection>
     </outputs>
     <tests>
-        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
         <test>
+            <param name="input">
+                <collection type="list">
+                    <element name="3722.faa" value="3722.faa"/>
+                    <element name="3722.fna" value="3722.fna"/>
+                    <element name="38889.faa" value="38889.faa"/>
+                    <element name="38889.fna" value="38889.fna"/>
+                    <element name="39614.faa" value="39614.faa"/>
+                    <element name="39614.fna" value="39614.fna"/>
+                </collection>
+            </param>
+            <param name="scaffold" value="22Gv1.1"/>
+            <param name="method" value="orthomcl"/>
+            <output_collection name="output" type="list">
+                <element name="3722.faa" file="3722_integrated.faa" ftype="fasta"/>
+                <element name="3722.fna" file="3722_integrated.fna" ftype="fasta"/>
+                <element name="38889.faa" file="38889_integrated.faa" ftype="fasta"/>
+                <element name="38889.fna" file="38889_integrated.fna" ftype="fasta"/>
+                <element name="39614.faa" file="39614_integrated.faa" ftype="fasta"/>
+                <element name="39614.fna" file="39614_integrated.fna" ftype="fasta"/>
+            </output_collection>
         </test>
-        -->
     </tests>
     <help>
 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary