--- a/ideas_preprocessor.xml	Wed Jan 24 09:55:28 2018 -0500
+++ b/ideas_preprocessor.xml	Wed Jan 24 10:16:04 2018 -0500
@@ -11,10 +11,10 @@
 #set tmp_dir = "tmp"
 #set ideaspre_input_config = "ideaspre_input_config.txt"
 #set ideas_input_config = "IDEAS_input_config.txt"
-#set specify_chrom_window = $specify_chrom_window_cond.specify_chrom_window
+#set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
 mkdir $tmp_dir &&
 mkdir $output.files_path &&
-#if str($specify_chrom_window) == "yes":
+#if str($specify_genomic_window) == "yes":
     ##############################################
     ## Using a genomic window bed file, so categorize
     ## the window positions by chromosome to enable
@@ -30,17 +30,19 @@
 sort $ideaspre_input_config -o $ideaspre_input_config &&
 Rscript '$__tool_directory__/ideas_preprocessor.R'
 --ideaspre_input_config '$ideaspre_input_config'
-#if str($specify_chrom_window) == "yes":
-    --chrom_bed_input '$specify_chrom_window_cond.chrom_bed_input'
+#if str($specify_genomic_window) == "yes":
+    --ideas_input_config '$ideas_input_config'
     --chromosome_windows '$chromosome_windows'
-    --ideas_input_config '$ideas_input_config'
+#end if
+#if str($specify_genomic_window) == "yes":
+    --bed_input '$specify_genomic_window_cond.bed_input'
 #else:
     --chrom_len_file '$chromInfo'
-    --window_size $specify_chrom_window_cond.window_size
-    #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes
+    --window_size $specify_genomic_window_cond.window_size
+    #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
     #if str($restrict_chromosomes) == "yes":
         #set chroms = []
-        #set chrom_repeat = $specify_chrom_window_cond.restrict_chromosomes_cond.chrom_repeat
+        #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
         #for $i in $chrom_repeat.chrom
             $chroms.append($i)
         #end for
@@ -84,10 +86,10 @@
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
     #end for
 #end if]]></configfile>
-        <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_chrom_window_cond.specify_chrom_window) == "yes":
+        <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
     #import collections
     #set window_positions_by_chroms_odict = $collections.OrderedDict()
-    #for count, line in enumerate(open($specify_chrom_window_cond.chrom_bed_input.file_name, 'r')):
+    #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
         #set $line = $line.strip()
         #if not $line or $line.startswith('#'):
             #continue
@@ -137,8 +139,8 @@
                 </repeat>
             </when>
         </conditional>
-        <conditional name="specify_chrom_window_cond">
-            <param name="specify_chrom_window" type="select" label="Specify window positions using a bed file?">
+        <conditional name="specify_genomic_window_cond">
+            <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
@@ -158,7 +160,7 @@
                 </conditional>
             </when>
             <when value="yes">
-                <param name="chrom_bed_input" type="data" format="bed" label="Bed file specifying the window positions"/>
+                <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/>
             </when>
         </conditional>
         <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>