--- a/ideas.xml	Thu Aug 10 13:13:15 2017 -0400
+++ b/ideas.xml	Thu Aug 10 14:09:11 2017 -0400
@@ -6,11 +6,16 @@
         <requirement type="package" version="332">ucsc-bedsort</requirement>
         <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
         <requirement type="package" version="1.2.0">ideas</requirement>
+        <requirement type="package" version="1.3.0">r-optparse</requirement>
     </requirements>
     <command><![CDATA[
 #import os
-mkdir -p tmp &&
-mkdir -p prep_output &&
+#set tmp_dir = 'tmp'
+#set prep_output_dir = 'prep_output'
+#set ideas_input_dir = 'ideas_input'
+#set ideas_matrix_input_file = $ideas_input_dir/r_matrix.txt
+mkdir -p $prep_output_dir &&
+mkdir -p $ideas_input_dir &&
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -53,17 +58,10 @@
 ##############################################
 ## 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'
+-i $tmp_dir/*.bed.gz
+-o $ideas_matrix_input_file
+-w $ideas_input_dir
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################
@@ -119,10 +117,10 @@
     -maxerr $set_max_standard_dev_cond.max_standard_dev
 #end if
 -thread \${GALAXY_SLOTS:-4}
--o 'prep_output'
-&& mv prep_output/*.state $output_state
-&& mv prep_output/*.para $output_para
-&& mv prep_output/*cluster $output_cluster
+-o $prep_output_dir
+&& mv $prep_output_dir/*.state $output_state
+&& mv $prep_output_dir/*.para $output_para
+&& mv $prep_output_dir/*cluster $output_cluster
     ]]></command>
     <configfiles>
         <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: