# HG changeset patch
# User greg
# Date 1503574860 14400
# Node ID cf0fbd58feb4e273a35493e8f373854327fc7bdf
# Parent  d89f1a065d5c682a4ed366e0985464b5746577cf
Uploaded

diff -r d89f1a065d5c -r cf0fbd58feb4 ideas.xml
--- a/ideas.xml	Wed Aug 23 15:11:44 2017 -0400
+++ b/ideas.xml	Thu Aug 24 07:41:00 2017 -0400
@@ -19,13 +19,9 @@
 #if str($input_type) == "datasets":
     #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
     #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
-    #if str($cell_type_epigenetic_factor) == "extract":
-        cp '$extract_prep_input_config' $prep_input_config &&
-    #else:
-        cp '$manual_prep_input_config' $prep_input_config &&
-    #end if
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
+    cp '$prep_input_config' $prep_input_config &&
     prepMat
     $prep_input_config
     #if str($specify_genomic_window) == "yes":
@@ -114,15 +110,13 @@
 && mv ./*.state $output_state
     ]]></command>
     <configfiles>
-        <configfile name="manual_prep_input_config"><![CDATA[
+        <configfile name="prep_input_config"><![CDATA[
+#import os
 #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
-#end if]]></configfile>
-        <configfile name="extract_prep_input_config"><![CDATA[
-#import os
-#if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
+#else if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract":
     #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
     #for $i in $cell_type_epigenetic_factor_cond.input: