--- a/ideas.xml	Fri Aug 11 13:24:23 2017 -0400
+++ b/ideas.xml	Mon Aug 14 08:31:13 2017 -0400
@@ -57,20 +57,25 @@
     -norm
 #end if
 ##############################################
+## Conform the prepMat config output to the
+## format expected by the R matrix builder.
+##############################################
+&& cut -d' ' $prep_input_config -f1,2 > file1.txt
+&& ls -p tmp/ | grep ".bed.gz" > file2.txt
+&& paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
+##############################################
 ## Build the R matrix from the prepMat output
 ##############################################
 ##&& Rscript '$__tool_directory__/build_matrix.R'
 ##-i $tmp_dir/*.bed.gz
 ##-o $ideas_matrix_input_file
 ##-w $ideas_input_dir
-&& cut -d' ' $prep_input_config -f1,2 > file1.txt
-&& ls -p tmp/ | grep ".bed.gz" > file2.txt
-&& paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
 ##############################################
 ## Run IDEAS on the R matrix
 ##############################################
 && ideas
 '$prep_output_config'
+$tmp_dir/*.bed
 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
 #if str($smoother_annotation) == 'yes':
     -hp
@@ -122,9 +127,10 @@
 #end if
 -thread \${GALAXY_SLOTS:-4}
 -o $prep_output_dir
-&& mv $prep_output_dir/*.state $output_state
+&& mv $prep_output_dir/*cluster $output_cluster
 && mv $prep_output_dir/*.para $output_para
-&& mv $prep_output_dir/*cluster $output_cluster
+&& mv $prep_output_dir/*.profile $output_profile
+&& mv $prep_output_dir/*.state $output_state
     ]]></command>
     <configfiles>
         <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
@@ -284,9 +290,10 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
+        <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>
+        <data name="output_profile" format="txt" label="${tool.name} (profile) on ${on_string}"/>
         <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/>
-        <data name="output_para" format="txt" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>
-        <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
     </outputs>
     <tests>
     </tests>