# HG changeset patch
# User greg
# Date 1503513390 14400
# Node ID 7abcf1870e3993e1b6fb833ef8c00dc82852404a
# Parent  7d5b11f4d00d44de8609c021b265c58645552b61
Uploaded

diff -r 7d5b11f4d00d -r 7abcf1870e39 ideas.xml
--- a/ideas.xml	Wed Aug 23 14:29:25 2017 -0400
+++ b/ideas.xml	Wed Aug 23 14:36:30 2017 -0400
@@ -23,13 +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':
-        #set prep_input_config = '$extract_prep_input_config'
+        '$extract_prep_input_config' &&
+        cp '$extract_prep_input_config' "prep_input_config.txt" &&
     #else:
-        #set prep_input_config = '$manual_prep_input_config'
+        '$manual_prep_input_config' &&
+        cp '$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
-    cp $prep_input_config "prep_input_config.txt" &&
     prepMat
     #if str($specify_genomic_window) == 'yes':
         -bed '$specify_genomic_window_cond.bed_input'
@@ -57,7 +58,7 @@
 ## Coerce the prepMat config output to the
 ## format expected by the R matrix builder.
 ##############################################
-&& cut -d' ' $prep_input_config -f1,2 > file1.txt
+&& cut -d' ' prep_input_config.txt -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################