--- a/fasta_extract.xml	Sun Jan 10 14:15:26 2016 -0500
+++ b/fasta_extract.xml	Sun Jan 10 14:15:34 2016 -0500
@@ -7,6 +7,7 @@
     <command>
         <![CDATA[
             mkdir -p output_dir &&
+            mkdir -p output_orphan_dir &&
             python $__tool_directory__/fasta_extract.py
             #for $i in $inputs:
                 --input "$i" "${i.hid}"
@@ -54,7 +55,10 @@
         </param>
     </inputs>
     <outputs>
-        <collection name="fasta_extract_output" type="list" label="Extract fasta sequences ${on_string}">
+        <collection name="fasta_extract_output_orphan" type="list" label="Extract fasta sequences (orphans) on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_orphan_dir" ext="gff" visible="false" />
+        </collection>
+        <collection name="fasta_extract_output" type="list" label="Extract fasta sequences on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output_dir" ext="fasta" visible="false" />
         </collection>
     </outputs>