# HG changeset patch
# User greg
# Date 1513093646 18000
# Node ID 8ce93420010c0aae2a9fbe91099884130e642d09
# Parent  5150fcdcd0fa4e5c0bb65783aeff1a634d4c311b
Uploaded

diff -r 5150fcdcd0fa -r 8ce93420010c ideas.xml
--- a/ideas.xml	Tue Dec 12 10:13:26 2017 -0500
+++ b/ideas.xml	Tue Dec 12 10:47:26 2017 -0500
@@ -18,7 +18,9 @@
 ## Create the config file and prepare the data
 ##############################################
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-mkdir '$output_pdf_dir' &&
+#if str($output_heatmaps) == "yes":
+    mkdir '$output_pdf_dir' &&
+#end if
 mkdir '$output_txt_dir' &&
 cp '$gen_prep_input_config' $prep_input_config &&
 prepMat
@@ -56,12 +58,12 @@
 && cut -d' ' $prep_input_config -f1,2 > file1.txt
 && ls tmp/*.bed.gz > file2.txt
 && paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
-##############################################
-## If using a genomic window bed file, categorize
-## the window positions by chromosome to enable
-## the IDEAS -inv option.
-##############################################
 #if str($specify_genomic_window) == "yes":
+    ##############################################
+    ## Using a genomic window bed file, so categorize
+    ## the window positions by chromosome to enable
+    ## the IDEAS -inv option.
+    ##############################################
     #import collections
     #set window_positions_by_chroms = collections.OrderedDict()
     #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
@@ -127,6 +129,9 @@
 
     #end for
 #else:
+    ##############################################
+    ## Not using a genomic window bed file.
+    ##############################################
     && ideas
     '$prep_output_config'
     $tmp_dir/*.bed