--- a/ideas.xml	Tue Nov 14 10:40:10 2017 -0500
+++ b/ideas.xml	Wed Nov 15 07:36:55 2017 -0500
@@ -12,7 +12,7 @@
 #set output_dir = "output_dir"
 #set tmp_dir = "tmp"
 #set prep_input_config = "prep_input_config.txt"
-#set prep_output_config = "prep_output_config.txt"
+#set prep_output_config = '$project_name'
 ##############################################
 ## Create the config file and prepare the data
 ##############################################
@@ -154,6 +154,7 @@
                 </repeat>
             </when>
         </conditional>
+        <param name="project_name" type="text" value="" optional="false" label="Project name" help="Output datasets will have this base name"/>
         <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/>
         <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">
@@ -290,6 +291,7 @@
   * **Epigenetic factor name** - epigenetic factor name
   * **BAM or BigWig file** - BAM or BigWig file
 
+* **Project name** - datasets produced by IDEAS will have this base name.
 * **Seed for IDEAS model initialization** - enter an integer to be used as the seed for the IDEAS model initialization.  A zero value causes IDEAS to automatically generate a random seed, and this seed will be different for each job run.
 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation.  If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file.  This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used.