--- a/ideas_preprocessor.xml	Tue Jan 23 10:48:38 2018 -0500
+++ b/ideas_preprocessor.xml	Wed Jan 24 08:29:58 2018 -0500
@@ -9,40 +9,40 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set tmp_dir = "tmp"
-#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 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
 mkdir $tmp_dir &&
 mkdir $output.files_path &&
-#if str($specify_genomic_window) == "yes":
+#if str($specify_chrom_window) == "yes":
     ##############################################
     ## Using a genomic window bed file, so categorize
     ## the window positions by chromosome to enable
     ## the IDEAS -inv option.
     ##############################################
-    #set windows_positions_by_chroms_config = "windows_positions_by_chroms_config.txt"
-    cp '$gen_windows_positions_by_chroms_config' $windows_positions_by_chroms_config &&
+    #set chromosome_windows = "chromosome_windows.txt"
+    cp '$gen_chromosome_windows' $chromosome_windows &&
 #end if
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
-cp '$gen_prep_input_config' $prep_input_config &&
-sort $prep_input_config -o $prep_input_config &&
+cp '$gen_ideaspre_input_config' $ideaspre_input_config &&
+sort $ideaspre_input_config -o $ideaspre_input_config &&
 Rscript '$__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'
+--ideaspre_input_config '$ideaspre_input_config'
+#if str($specify_chrom_window) == "yes":
+    --ideas_input_config '$ideas_input_config'
+    --chromosome_windows '$chromosome_windows'
 #end if
-#if str($specify_genomic_window) == "yes":
-    --bed_input '$specify_genomic_window_cond.bed_input'
+#if str($specify_chrom_window) == "yes":
+    --chrom_bed_input '$specify_chrom_window_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_window_cond.window_size
+    #set restrict_chromosomes = $specify_chrom_window_cond.restrict_chromosomes_cond.restrict_chromosomes
     #if str($restrict_chromosomes) == "yes":
         #set chroms = []
-        #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
+        #set chrom_repeat = $specify_chrom_window_cond.restrict_chromosomes_cond.chrom_repeat
         #for $i in $chrom_repeat.chrom
             $chroms.append($i)
         #end for
@@ -54,6 +54,7 @@
     --exclude_input '$exclude_input'
 #end if
 --output '$output'
+--output_hid $output.hid
 --output_files_path '$output.files_path'
 &> ideas_preprocessor_log.txt;
 if [[ $? -ne 0 ]]; then
@@ -62,7 +63,7 @@
 fi
     ]]></command>
     <configfiles>
-        <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
+        <configfile name="gen_ideaspre_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
     #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
     #for $i in $cell_type_epigenetic_factor_cond.input:
         #set file_name_with_ext = $i.name
@@ -85,10 +86,10 @@
 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} ${file_name} ${input_items.input.ext}
     #end for
 #end if]]></configfile>
-        <configfile name="gen_windows_positions_by_chroms_config"><![CDATA[#if str($specify_genomic_window_cond.specify_genomic_window) == "yes":
+        <configfile name="gen_chromosome_windows"><![CDATA[#if str($specify_chrom_window_cond.specify_chrom_window) == "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_window_cond.chrom_bed_input.file_name, 'r')):
         #set $line = $line.strip()
         #if not $line or $line.startswith('#'):
             #continue
@@ -138,8 +139,8 @@
                 </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_window_cond">
+            <param name="specify_chrom_window" type="select" label="Specify window positions using a bed file?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
@@ -159,7 +160,7 @@
                 </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 specifying the window positions"/>
             </when>
         </conditional>
         <param argument="--bychr" type="boolean" truevalue="true" falsevalue="" checked="False" label="Output chromosomes in separate files"/>
@@ -171,7 +172,7 @@
         <param argument="--standardize_datasets" type="boolean" truevalue="true" falsevalue="" checked="False" label="Standardize all datasets"/>
     </inputs>
     <outputs>
-        <data name="output" format="html"/>
+        <data name="output" format="ideaspre"/>
     </outputs>
     <tests>
         <test>