--- a/ideas_preprocessor.xml	Wed Jan 31 08:22:43 2018 -0500
+++ b/ideas_preprocessor.xml	Wed Jan 31 14:13:11 2018 -0500
@@ -11,6 +11,8 @@
 #set chromosome_windows = "chromosome_windows.txt"
 #set ideaspre_input_config = "ideaspre_input_config.txt"
 #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_chrom_windows) == "yes":
     ##############################################
@@ -179,8 +181,13 @@
         <test>
             <param name="input" value="e001-h3k4me3.bigwig" ftype="bigwig" dbkey="hg19"/>
             <param name="specify_chrom_windows" value="yes"/>
-            <param name="chrom_bed_input" value="chrom_windows.bed" ftype="bed" dbkey="hg19"/>
-            <output name="output" file="output.ideaspre" ftype="ideaspre" />
+            <param name="chrom_bed_input" value="chromosomes.bed" ftype="bed" dbkey="hg19"/>
+            <output name="output" file="output.html" ftype="ideaspre">
+                <extra_files type="file" name="chromosomes.bed" value="chromosomes.bed"/>
+                <extra_files type="file" name="chromosome_windows.txt" value="chromosome_windows.txt"/>
+                <extra_files type="file" name="IDEAS_input_config.txt" value="IDEAS_input_config.txt"/>
+                <extra_files type="file" name="tmp.tar" value="tmp.tar" compare="sim_size"/>
+            </output>
         </test>
     </tests>
     <help>