# HG changeset patch
# User greg
# Date 1510665753 18000
# Node ID dad89ec8846fb384a8bd3d4ce2fdb06aab032461
# Parent  ad45c3ba16b215bb3d8cf36d0cd1184641974ae4
Uploaded

diff -r ad45c3ba16b2 -r dad89ec8846f ideas.xml
--- a/ideas.xml	Wed Nov 08 07:45:52 2017 -0500
+++ b/ideas.xml	Tue Nov 14 08:22:33 2017 -0500
@@ -91,10 +91,6 @@
 #else:
     > /dev/null
 #end if
-&& mv ./*.cluster $output_cluster
-&& mv ./*.para $output_para
-&& mv ./*.profile $output_profile
-&& mv ./*.state $output_state
     ]]></command>
     <configfiles>
         <configfile name="gen_prep_input_config"><![CDATA[#import os
@@ -199,13 +195,12 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output_log" format="txt" label="${tool.name} (ideas output log) on ${on_string}">
+        <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
             <filter>save_ideas_log == 'yes'</filter>
         </data>
-        <data name="output_cluster" format="txt" label="${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}"/>
+        <collection name="output" type="list">
+            <discover_datasets pattern="__name__" format="txt"/>
+        </collection>
     </outputs>
     <tests>
         <test>
@@ -216,8 +211,14 @@
             <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.tabular" ftype="tabular"/>
+            <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>
+
         </test>
         <test>
             <param name="cell_type_epigenetic_factor" value="manual"/>
@@ -230,7 +231,7 @@
             <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.tabular" ftype="tabular"/>
+            <output name="output_para" file="output_para.txt" ftype="txt"/>
             <output name="output_cluster" file="output_cluster.txt" ftype="txt"/>
         </test>
     </tests>