--- a/ideas_preprocessor.xml	Wed Jan 24 13:47:23 2018 -0500
+++ b/ideas_preprocessor.xml	Wed Jan 24 14:04:47 2018 -0500
@@ -45,9 +45,15 @@
         --restrict_to_chroms ",".join(chroms)
     #end if
 #end if
+#if str($bychr) == "true":
+    --bychr true
+#end if
 --reads_per_bp $reads_per_bp
-#if str($exclude_input) not in ["None", ""]:
-    --exclude_input '$exclude_input'
+#if str($exclude_bed_input) not in ["None", ""]:
+    --exclude_bed_input '$exclude_bed_input'
+#end if
+#if str($standardize_datasets) == "true":
+    --standardize_datasets true
 #end if
 --output '$output'
 --output_hid $output.hid
@@ -156,7 +162,7 @@
                 </conditional>
             </when>
             <when value="yes">
-                <param name="chrom_bed_input" type="data" format="bed" label="Bed file for defining the chromosome window positions">
+                <param name="chrom_bed_input" type="data" format="bed" label="Select bed file for defining chromosome window positions">
                     <validator type="empty_dataset"/>
                 </param>
             </when>
@@ -166,7 +172,7 @@
             <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 name="exclude_bed_input" type="data" format="bed" optional="True" multiple="True" label="Select bed file(s) containing regions to exclude"/>
         <param name="standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
     </inputs>
     <outputs>