--- a/ideas.xml	Fri Aug 11 09:53:42 2017 -0400
+++ b/ideas.xml	Fri Aug 11 13:24:23 2017 -0400
@@ -12,6 +12,7 @@
 #import os
 #set tmp_dir = 'tmp'
 #set prep_output_dir = 'prep_output'
+#set prep_output_config = 'prep_output_config.txt'
 #set ideas_input_dir = 'ideas_input'
 #set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt')
 mkdir -p $prep_output_dir &&
@@ -20,10 +21,10 @@
 ## Create the config file and prepare the data
 ##############################################
 #set input_type = $input_type_cond.input_type
-cp '$build_config_file' 'config_file.txt' &&
+cp '$prep_input_config' 'prep_input_config.txt' &&
 prepMat
 #if str($input_type) == 'datasets':
-    '$build_config_file'
+    '$prep_input_config'
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     #if str($specify_genomic_window) == 'yes':
@@ -58,15 +59,18 @@
 ##############################################
 ## Build the R matrix from the prepMat output
 ##############################################
-&& Rscript '$__tool_directory__/build_matrix.R'
--i $tmp_dir/*.bed.gz
--o $ideas_matrix_input_file
--w $ideas_input_dir
+##&& Rscript '$__tool_directory__/build_matrix.R'
+##-i $tmp_dir/*.bed.gz
+##-o $ideas_matrix_input_file
+##-w $ideas_input_dir
+&& cut -d' ' $prep_input_config -f1,2 > file1.txt
+&& ls -p tmp/ | grep ".bed.gz" > file2.txt
+&& paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################
 && ideas
-'$build_config_file'
+'$prep_output_config'
 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
 #if str($smoother_annotation) == 'yes':
     -hp
@@ -123,7 +127,7 @@
 && mv $prep_output_dir/*cluster $output_cluster
     ]]></command>
     <configfiles>
-        <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
+        <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
 #end for ]]></configfile>
     </configfiles>