--- a/ideas_preprocessor.xml	Wed Jan 24 10:18:39 2018 -0500
+++ b/ideas_preprocessor.xml	Wed Jan 24 13:47:16 2018 -0500
@@ -8,19 +8,18 @@
         <requirement type="package" version="357">ucsc-bigwigaverageoverbed</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-#set tmp_dir = "tmp"
+#set chromosome_windows = "chromosome_windows.txt"
 #set ideaspre_input_config = "ideaspre_input_config.txt"
-#set ideas_input_config = "IDEAS_input_config.txt"
-#set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
+#set specify_chrom_windows = $specify_chrom_windows_cond.specify_chrom_windows
+#set tmp_dir = "tmp"
 mkdir $tmp_dir &&
 mkdir $output.files_path &&
-#if str($specify_genomic_window) == "yes":
+#if str($specify_chrom_windows) == "yes":
     ##############################################
-    ## Using a genomic window bed file, so categorize
-    ## the window positions by chromosome to enable
-    ## the IDEAS -inv option.
+    ## Using a bed file for defining chrom windows,
+    ## so categorize the window positions by
+    ## chromosome to enable the IDEAS -inv option.
     ##############################################
-    #set chromosome_windows = "chromosome_windows.txt"
     cp '$gen_chromosome_windows' $chromosome_windows &&
 #end if
 ##############################################
@@ -30,19 +29,16 @@
 sort $ideaspre_input_config -o $ideaspre_input_config &&
 Rscript '$__tool_directory__/ideas_preprocessor.R'
 --ideaspre_input_config '$ideaspre_input_config'
-#if str($specify_genomic_window) == "yes":
-    --ideas_input_config '$ideas_input_config'
+#if str($specify_chrom_windows) == "yes":
     --chromosome_windows '$chromosome_windows'
-#end if
-#if str($specify_genomic_window) == "yes":
-    --bed_input '$specify_genomic_window_cond.bed_input'
+    --chrom_bed_input '$specify_chrom_windows_cond.chrom_bed_input'
 #else:
     --chrom_len_file '$chromInfo'
-    --window_size $specify_genomic_window_cond.window_size
-    #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
+    --window_size $specify_chrom_windows_cond.window_size
+    #set restrict_chromosomes = $specify_chrom_windows_cond.restrict_chromosomes_cond.restrict_chromosomes
     #if str($restrict_chromosomes) == "yes":
         #set chroms = []
-        #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
+        #set chrom_repeat = $specify_chrom_windows_cond.restrict_chromosomes_cond.chrom_repeat
         #for $i in $chrom_repeat.chrom
             $chroms.append($i)
         #end for
@@ -59,7 +55,7 @@
 &> ideas_preprocessor_log.txt;
 if [[ $? -ne 0 ]]; then
     cp ideas_preprocessor_log.txt '$output';
-    exit 1;
+   exit 1;
 fi
     ]]></command>
     <configfiles>
@@ -86,10 +82,10 @@
 ${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_genomic_window_cond.specify_genomic_window) == "yes":
+        <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_chrom_windows_cond.specify_chrom_windows) == "yes":
     #import collections
     #set window_positions_by_chroms_odict = $collections.OrderedDict()
-    #for count, line in enumerate(open($specify_genomic_window_cond.bed_input.file_name, 'r')):
+    #for count, line in enumerate(open($specify_chrom_windows_cond.chrom_bed_input.file_name, 'r')):
         #set $line = $line.strip()
         #if not $line or $line.startswith('#'):
             #continue
@@ -139,8 +135,8 @@
                 </repeat>
             </when>
         </conditional>
-        <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">
+        <conditional name="specify_chrom_windows_cond">
+            <param name="specify_chrom_windows" type="select" label="Define chromosome window positions from a bed file?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
@@ -160,16 +156,18 @@
                 </conditional>
             </when>
             <when value="yes">
-                <param name="bed_input" type="data" format="bed" label="Bed file specifying the genomic windows"/>
+                <param name="chrom_bed_input" type="data" format="bed" label="Bed file for defining the chromosome window positions">
+                    <validator type="empty_dataset"/>
+                </param>
             </when>
         </conditional>
-        <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
-        <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each genomic window using">
+        <param name="bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
+        <param name="reads_per_bp" type="select" display="radio" label="Calculate the signal in each window using">
             <option value="6" selected="true">mean</option>
             <option value="8">max</option>
         </param>
         <param name="exclude_input" type="data" format="bed" optional="True" multiple="True" label="Select file(s) containing regions to exclude"/>
-        <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
+        <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
     </inputs>
     <outputs>
         <data name="output" format="ideaspre"/>