# HG changeset patch
# User greg
# Date 1510667249 18000
# Node ID 705c4f8fbefd614d1fa1a0fdd75e33ca14b0b0ff
# Parent  dad89ec8846fb384a8bd3d4ce2fdb06aab032461
Uploaded

diff -r dad89ec8846f -r 705c4f8fbefd ideas.xml
--- a/ideas.xml	Tue Nov 14 08:22:33 2017 -0500
+++ b/ideas.xml	Tue Nov 14 08:47:29 2017 -0500
@@ -16,6 +16,7 @@
 ## Create the config file and prepare the data
 ##############################################
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
+mkdir $output_dir &&
 cp '$gen_prep_input_config' $prep_input_config &&
 prepMat
 $prep_input_config
@@ -91,6 +92,10 @@
 #else:
     > /dev/null
 #end if
+&& mv ./*.cluster output_dir
+&& mv ./*.para output_dir
+&& mv ./*.profile output_dir
+&& mv ./*.state output_dir
     ]]></command>
     <configfiles>
         <configfile name="gen_prep_input_config"><![CDATA[#import os
@@ -199,7 +204,7 @@
             <filter>save_ideas_log == 'yes'</filter>
         </data>
         <collection name="output" type="list">
-            <discover_datasets pattern="__name__" format="txt"/>
+            <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
         </collection>
     </outputs>
     <tests>