# HG changeset patch
# User greg
# Date 1502382892 14400
# Node ID 9874800487e63cff522a3861e48394ce30745063
# Parent  7a77ec6342c12a52cda646615dce9ef6274eca22
Uploaded

diff -r 7a77ec6342c1 -r 9874800487e6 ideas.xml
--- a/ideas.xml	Thu Aug 10 12:34:42 2017 -0400
+++ b/ideas.xml	Thu Aug 10 12:34:52 2017 -0400
@@ -8,8 +8,11 @@
         <requirement type="package" version="1.2.0">ideas</requirement>
     </requirements>
     <command><![CDATA[
+#import os
 mkdir -p tmp &&
+##############################################
 ## Create the config file and prepare the data
+##############################################
 #set input_type = $input_type_cond.input_type
 cp '$build_config_file' 'config_file.txt' &&
 prepMat
@@ -46,7 +49,23 @@
 #if str($standardize_datasets) == 'yes':
     -norm
 #end if
-## Run IDEAS on the prepared data
+##############################################
+## Build the R matrix from the prepMat output
+##############################################
+#set r_matrix_input = None
+#for f in $os.listdir(tmp):
+    #if f.endswith('.bed.gz'):
+        #set r_matrix_input = $os.path.join(tmp, f)
+    #end if
+#end for
+#assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty."
+&& Rscript '$__tool_directory__/build_matrix.R'
+-i $r_matrix_input
+-o '%s.input' % $f
+-w 'tmp'
+##############################################
+## Run IDEAS on the R matrix
+##############################################
 && mkdir -p output
 && ideas
 '$build_config_file'