# HG changeset patch
# User greg
# Date 1503512229 14400
# Node ID af8bf2b76697bf1c81b78dfbf4748764a30a06d4
# Parent  c9c90bfbeb200944cf86fea29beebb36a39301a3
Uploaded

diff -r c9c90bfbeb20 -r af8bf2b76697 ideas.xml
--- a/ideas.xml	Wed Aug 23 14:07:10 2017 -0400
+++ b/ideas.xml	Wed Aug 23 14:17:09 2017 -0400
@@ -19,17 +19,17 @@
 ## Create the config file and prepare the data
 ##############################################
 #set input_type = $input_type_cond.input_type
-prepMat
 #if str($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':
-        '$extract_prep_input_config'
+        #set prep_input_config = '$extract_prep_input_config'
     #else:
-        '$manual_prep_input_config'
+        #set prep_input_config = '$manual_prep_input_config'
     #end if
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
+    prepMat
     #if str($specify_genomic_window) == 'yes':
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
@@ -56,7 +56,7 @@
 ## Coerce the prepMat config output to the
 ## format expected by the R matrix builder.
 ##############################################
-&& cut -d' ' $manual_prep_input_config -f1,2 > file1.txt
+&& cut -d' ' $prep_input_config -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################
@@ -117,7 +117,7 @@
     ]]></command>
     <configfiles>
         <configfile name="manual_prep_input_config"><![CDATA[
-#for $input_items in $input_type_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]]></configfile>
         <configfile name="extract_prep_input_config"><![CDATA[