--- a/yolo.xml	Tue Oct 17 11:31:47 2017 -0400
+++ b/yolo.xml	Tue Oct 17 13:28:44 2017 -0400
@@ -4,26 +4,36 @@
         <requirement type="package" version="1.0">darknet</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+mkdir output_shape_confidence_dir &&
 mkdir input_dir &&
-mkdir output_dir &&
+mkdir output_png_dir &&
 cp -R /home/greg/_conda/envs/__darknet@1.0/bin/* .
 #for $i in $input:
     #set input_filename = $i.file_name
     #set full_name = $i.name
     #set head = $full_name.split('.')[0]
-    #set output_filename = '%s_predictions.png' % $head
+    #set output_filename_png = '%s_predictions.png' % $head
+    #set output_filename_shape_confidence = '%s_shape_detection_confidence.tabular' % $head
     && ln -s $input_filename input_dir/$full_name
-    && darknet detect cfg/yolo.cfg yolo.weights 'input_dir/$full_name' -thresh $thresh 2> /dev/null
-    && mv ./predictions.png output_dir/$output_filename
+    && darknet detect cfg/yolo.cfg yolo.weights 'input_dir/$full_name' -thresh $thresh > output_shape_confidence_dir/$set output_filename_shape_confidence
+    && mv ./predictions.png output_png_dir/$output_filename_png
 #end for
     ]]></command>
     <inputs>
         <param name="input" format="jpg" type="data_collection" collection_type="list" label="Collection of image files" />
         <param name="thresh" type="float" value="0.25" label="Object detection threshold" />
+        <param name="output_shape_confidence" type="select" display="radio" label="Output shape detection confidence levels?">
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+        </param>
     </inputs>
     <outputs>
-        <collection name="output" type="list">
-            <discover_datasets pattern="__name__" directory="output_dir" format="png" />
+        <collection name="output_shape" type="list" label="${tool.name} (shapes) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_png_dir" format="png" />
+        </collection>
+        <collection name="output_shape_confidence" type="list" label="${tool.name} (shape detection confidence) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_shape_confidence_dir" format="tabular" />
+            <filter>output_shape_confidence == 'yes'</filter>
         </collection>
     </outputs>
     <tests>