# HG changeset patch
# User jbrayet
# Date 1453391150 18000
# Node ID e07fc2fd6bdc9a4aa8211aaa3dfa347f22f63ccb
# Parent  876655b15db41b161a94ac8293ed619eee00b1ac
Uploaded

diff -r 876655b15db4 -r e07fc2fd6bdc ccat_wrapper.xml
--- a/ccat_wrapper.xml	Thu Jan 21 10:41:22 2016 -0500
+++ b/ccat_wrapper.xml	Thu Jan 21 10:45:50 2016 -0500
@@ -7,7 +7,7 @@
   #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
   '$input_advanced_config_file' 
   #else:
-  '$options_type.input_config_file'
+  ${options_type[ 'options_type.input_config_file' ]}
   #end if
   'CCAT' 
   '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file' '${__root_dir__}'</command>
@@ -45,9 +45,27 @@
     </conditional>
 </inputs>
   <outputs>
-    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" />
-    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" />
-    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)" />
+    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
     <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
   </outputs>
   <configfiles>