# HG changeset patch
# User greg
# Date 1503512491 14400
# Node ID 14ac679f3c4c0f408613339595d25659c7b958b2
# Parent  af8bf2b76697bf1c81b78dfbf4748764a30a06d4
Uploaded

diff -r af8bf2b76697 -r 14ac679f3c4c ideas.xml
--- a/ideas.xml	Wed Aug 23 14:17:09 2017 -0400
+++ b/ideas.xml	Wed Aug 23 14:21:31 2017 -0400
@@ -117,10 +117,13 @@
     ]]></command>
     <configfiles>
         <configfile name="manual_prep_input_config"><![CDATA[
+#if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual":
 #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
-#end for]]></configfile>
+#end for
+#end if]]></configfile>
         <configfile name="extract_prep_input_config"><![CDATA[
+#if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
 #!/bin/bash
 #set $cell_type_epigenetic_factor_cond=$input_type_cond.cell_type_epigenetic_factor_cond
 #set $input_name_positions=$cell_type_epigenetic_factor_cond.input_name_positions
@@ -136,7 +139,8 @@
         #set $epigenetic_factor_name="${file_name%-*}"
     #end if
 ${cell_type_name} ${epigenetic_factor_name} ${i}
-#end for]]></configfile>
+#end for
+#end if]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="input_type_cond">