# HG changeset patch
# User mgarnier
# Date 1625237680 0
# Node ID 27c5a6f2301c7b06f9766f79a092e9c73fbffac4
# Parent  0428ce25da814d8d31ba646e9ea52180e7704751
Uploaded

diff -r 0428ce25da81 -r 27c5a6f2301c pangenomeCogAnalysis.xml
--- a/pangenomeCogAnalysis.xml	Fri Jul 02 14:53:33 2021 +0000
+++ b/pangenomeCogAnalysis.xml	Fri Jul 02 14:54:40 2021 +0000
@@ -16,7 +16,8 @@
             #set $named_input_files = $named_input_files + ',' + $_input_file
         #end for
 
-	perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4 $output5
+	perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4
+
 	]]></command>
 
 
@@ -34,7 +35,13 @@
 	 <data format="tabular" name="output2" label="COG category count average per group"/>
 	 <data format="tabular" name="output3" label="Detailed COG category count values per group"/>
 	 <data format="tabular" name="output4" label="COG category count average"/>
-	 <data format="tabular" name="output5" label="Core-genes coordinates"/>
+	 <!--<data format="tabular" name="output5" label="Core-genes coordinates"/>-->
+	 <collection name="output5" type="list" label="Core-genes coordinates">
+    		<discover_datasets pattern="__name_and_ext__" directory="Core" />
+	</collection>
+	<collection name="output6" type="list" label="Group specific genes coordinates">
+                <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" />
+        </collection>
 </outputs>
 
 </tool>