--- a/ideas_preprocessor.xml	Mon Jan 22 14:35:28 2018 -0500
+++ b/ideas_preprocessor.xml	Tue Jan 23 10:48:31 2018 -0500
@@ -12,18 +12,29 @@
 #set prep_input_config = "prep_input_config.txt"
 #set prep_output_config = "prep_output_config.txt"
 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-#set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
+mkdir $tmp_dir &&
+mkdir $output.files_path &&
+#if str($specify_genomic_window) == "yes":
+    ##############################################
+    ## Using a genomic window bed file, so categorize
+    ## the window positions by chromosome to enable
+    ## the IDEAS -inv option.
+    ##############################################
+    #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
+    cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config &&
+#end if
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
-#set output_dir = $output_txt_dir
-#set tmp_dir = "tmp"
-mkdir '$output_txt_dir' &&
 cp '$gen_prep_input_config' $prep_input_config &&
 sort $prep_input_config -o $prep_input_config &&
 Rscript '$__tool_directory__/ideas_preprocessor.R'
 --prep_input_config '$prep_input_config'
 #if str($specify_genomic_window) == "yes":
+    --prep_output_config '$prep_output_config'
+    --windows_positions_by_chroms_config '$windows_positions_by_chroms_config'
+#end if
+#if str($specify_genomic_window) == "yes":
     --bed_input '$specify_genomic_window_cond.bed_input'
 #else:
     --chrom_len_file '$chromInfo'
@@ -39,7 +50,7 @@
     #end if
 #end if
 --reads_per_bp $reads_per_bp
-#if str($blacklist_input) not in ["None", ""]:
+#if str($exclude_input) not in ["None", ""]:
     --exclude_input '$exclude_input'
 #end if
 --output '$output'
@@ -49,21 +60,6 @@
     cp ideas_preprocessor_log.txt '$output';
     exit 1;
 fi
-##############################################
-## Coerce the prepMat config output to the
-## format expected by IDEAS.
-##############################################
-&& cut -d' ' $prep_input_config -f1,2 > file1.txt
-&& ls $tmp_dir/*.bed.gz > file2.txt
-&& paste <(cat file1.txt) <(cat file2.txt) -d' ' > $prep_output_config
-#if str($specify_genomic_window) == "yes":
-    ##############################################
-    ## Using a genomic window bed file, so categorize
-    ## the window positions by chromosome to enable
-    ## the IDEAS -inv option.
-    ##############################################
-    && cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config
-#end if
     ]]></command>
     <configfiles>
         <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
@@ -82,11 +78,11 @@
             #set cell_type_name = $file_name.split("-")[1]
             #set epigenetic_factor_name = $file_name.split("-")[0]
         #end if
-${cell_type_name} ${epigenetic_factor_name} ${i} ${i.filename} ${i.ext}
+${cell_type_name} ${epigenetic_factor_name} ${i} ${file_name} ${i.ext}
     #end for
 #else:
     #for $input_items in $cell_type_epigenetic_factor_cond.input_repeat:
-${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${input_items.input.filename} ${input_items.input.ext}
+${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
     #end for
 #end if]]></configfile>
         <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":