# HG changeset patch
# User greg
# Date 1503514723 14400
# Node ID 9fbd77da30438fc5377c7ac6073135712a53e8ec
# Parent  c2642e6cb30ee258ba11b66189faa681e6047851
Uploaded

diff -r c2642e6cb30e -r 9fbd77da3043 ideas.xml
--- a/ideas.xml	Wed Aug 23 14:51:09 2017 -0400
+++ b/ideas.xml	Wed Aug 23 14:58:43 2017 -0400
@@ -23,15 +23,14 @@
     #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':
-        '$extract_prep_input_config' &&
         cp '$extract_prep_input_config' "prep_input_config.txt" &&
     #else:
-        '$manual_prep_input_config' &&
         cp '$manual_prep_input_config' "prep_input_config.txt" &&
     #end if
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     prepMat
+    "prep_input_config.txt"
     #if str($specify_genomic_window) == 'yes':
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
@@ -120,27 +119,27 @@
     <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:
+    #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 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":
-#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:
-    #set $file_name_with_ext = $os.path.basename($i)
-    #set $file_name = $file_name_with_ext.split('.')[0]
-    #if $input_name_positions == "cell_first":
-        #set $cell_type_name = $file_name.split('-')[0]
-        #set $epigenetic_factor_name = $file_name.split('-')[1]
-    #else:
-        #set $cell_type_name = $file_name.split('-')[1]
-        #set $epigenetic_factor_name = $file_name.split('-')[0]
-    #end if
+    #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:
+        #set $file_name_with_ext = $os.path.basename($i)
+        #set $file_name = $file_name_with_ext.split('.')[0]
+        #if $input_name_positions == "cell_first":
+            #set $cell_type_name = $file_name.split('-')[0]
+            #set $epigenetic_factor_name = $file_name.split('-')[1]
+        #else:
+            #set $cell_type_name = $file_name.split('-')[1]
+            #set $epigenetic_factor_name = $file_name.split('-')[0]
+        #end if
 ${cell_type_name} ${epigenetic_factor_name} ${i}
-#end for
+    #end for
 #end if]]></configfile>
     </configfiles>
     <inputs>