--- a/ideas.xml	Wed Nov 15 07:50:11 2017 -0500
+++ b/ideas.xml	Wed Nov 15 08:57:21 2017 -0500
@@ -88,6 +88,7 @@
 #end if
 -rseed $rseed
 -thread \${GALAXY_SLOTS:-4}
+-o '$project_name'
 #if str($save_ideas_log) == "yes":
     > $output_log
 #else:
@@ -154,6 +155,9 @@
                 </repeat>
             </when>
         </conditional>
+        <param name="project_name" type="text" value="" optional="false" label="Project name" help="Outputs will have this base name">
+            <validator type="empty_field"/>
+        </param>
         <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed, and this seed will be different for each job run."/>
         <conditional name="specify_genomic_window_cond">
             <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
@@ -207,7 +211,7 @@
             <filter>save_ideas_log == 'yes'</filter>
         </data>
         <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/>
-        <collection name="output" type="list">
+        <collection name="output_txt_collection" type="list">
             <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
         </collection>
     </outputs>
@@ -218,15 +222,13 @@
             <param name="input_name_positions" value="cell_first"/>
             <param name="specify_genomic_window" value="yes"/>
             <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
-            <output name="output_state" file="output_state.txt" ftype="txt"/>
-            <output name="output_profile" file="output_profile.txt" ftype="txt"/>
-            <output name="output_para" file="output_para.txt" ftype="txt"/>
-            <output name="output_cluster" file="output_cluster.txt" ftype="txt"/>
-            <output_collection name="primary_fna" type="list">
-                <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
-                <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
-                <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
+            <output_collection name="output_txt_collection" type="list">
+                <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
+                <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
+                <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
+                <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
             </output_collection>
+            <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
         </test>
         <test>
             <param name="cell_type_epigenetic_factor" value="manual"/>
@@ -237,10 +239,13 @@
             </repeat>
             <param name="specify_genomic_window" value="yes"/>
             <param name="bed_input" value="genomic_windows.bed" ftype="bed" dbkey="hg19"/>
-            <output name="output_state" file="output_state.txt" ftype="txt"/>
-            <output name="output_profile" file="output_profile.txt" ftype="txt"/>
-            <output name="output_para" file="output_para.txt" ftype="txt"/>
-            <output name="output_cluster" file="output_cluster.txt" ftype="txt"/>
+            <output_collection name="output_txt_collection" type="list">
+                <element name="IDEAS_out.cluster" file="IDEAS_out.cluster" ftype="txt"/>
+                <element name="IDEAS_out.parae" file="IDEAS_out.para" ftype="txt"/>
+                <element name="IDEAS_out.profile" file="IDEAS_out.profile" ftype="txt"/>
+                <element name="IDEAS_out.state" file="IDEAS_out.state" ftype="txt"/>
+            </output_collection>
+            <output name="output_heatmap" file="output_heatmap.pdf" ftype="pdf"/>
         </test>
     </tests>
     <help>