--- a/ideas.xml	Tue Aug 22 14:24:34 2017 -0400
+++ b/ideas.xml	Wed Aug 23 08:45:14 2017 -0400
@@ -26,7 +26,7 @@
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
     #if str($specify_genomic_window) == 'yes':
-        -bed '$bed_input'
+        -bed '$specify_genomic_window_cond.bed_input'
     #else:
         -gsz '$chromInfo'
         -wsz $specify_genomic_window_cond.window_size
@@ -73,14 +73,7 @@
 && ideas
 '$prep_output_config'
 $tmp_dir/*.bed
-#set smoother_annotation = $smoother_annotation_cond.smoother_annotation
-#if str($smoother_annotation) == 'yes':
-    -hp
-#end if
-#set smoother_annotation = $smoother_annotation_cond.smoother_annotation
-#if str($smoother_annotation) == 'yes':
-    -hp
-#end if
+$hp
 #if str($log2_num) != '0.0':
     -log2 $log2_num
 #end if
@@ -165,7 +158,7 @@
             <when value="data_matrix"/>
         </conditional>
         <conditional name="outputs_by_chr_cond">
-            <param name="outputs_by_chr" type="select" display="radio" label="Output chromosomes in seperate files">
+            <param name="outputs_by_chr" type="select" display="radio" label="Output chromosomes in separate files">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
@@ -185,14 +178,7 @@
             <when value="no"/>
             <when value="yes"/>
         </conditional>
-        <conditional name="smoother_annotation_cond">
-            <param name="smoother_annotation" type="select" display="radio" label="Discourage state transition across chromosomes">
-                <option value="no" selected="true">No</option>
-                <option value="yes">Yes</option>
-            </param>
-            <when value="no"/>
-            <when value="yes"/>
-        </conditional>
+        <param argument="-hp" type="boolean" truevalue="-hp" falsevalue="" checked="False" label="Discourage state transition across chromosomes"/>
         <param name="log2_num" type="float" value="0" min="0" label="Use log2(x+number) transformation" help="Zero value has no affect"/>
         <param name="max_states" type="float" value="0" min="0" label="Maximum number of states to be inferred" help="Zero value has no affect"/>
         <param name="initial_states" type="integer" value="20" min="1" label="Initial number of states" help="Zero value has no affect"/>
@@ -246,7 +232,7 @@
 
 **Other options**
 
-* **Output chromosomes in seperate files** - select "Yes" to produce seperate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
+* **Output chromosomes in separate files** - select "Yes" to produce separate files for each chromosome, allowing you to run IDEAS on different chromosomes separately.
 * **Calculate the average signal in each genomic window using** - use the bigWigAverageOverBed utility from the UCSC genome browser to calculate average signal (number of reads per bp) in each genomic window.
 * **Select file(s) containing regions to exclude** - select one or more bed files that contains regions you'd like excluded from your datasets.
 * **Standardize all datasets** - select "Yes" to standardize all datasets (e.g., reads / total_reads * 20 million) so that the signals from different cell types become comparable - your datasets can be read counts, logp-values or fold change.