# HG changeset patch
# User mgarnier
# Date 1625253936 0
# Node ID 3f4e4e7d77ffffc06571409bc67fc77323ece64b
# Parent  cf9da93e4145f01d057cbe069b8ea301a55db263
Uploaded

diff -r cf9da93e4145 -r 3f4e4e7d77ff pangenomeCogAnalysis.xml
--- a/pangenomeCogAnalysis.xml	Fri Jul 02 19:25:25 2021 +0000
+++ b/pangenomeCogAnalysis.xml	Fri Jul 02 19:25:36 2021 +0000
@@ -12,11 +12,11 @@
         #for $input_file in $input_files
             ## Add single quotes around each input file identifier
             #set $_input_file = "'{}'".format($input_file.element_identifier)
-            ln -s '${input_file}' ${_input_file} &&
+            ##ln -s '${input_file}' ${_input_file} &&
             #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
+	perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $input_files $named_input_files $gff_files $output $output2 $output3 $output4
 
 	]]></command>
 
@@ -37,11 +37,8 @@
 	 <data format="tabular" name="output4" label="COG category count average"/>
 	 <!--<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" />
+    		<discover_datasets pattern="__name_and_ext__" directory="SampleDataset" />
 	</collection>
-	<collection name="output6" type="list" label="Group specific genes coordinates">
-                <discover_datasets pattern="__name_and_ext__" directory="GroupSpecific" />
-        </collection>
 </outputs>
 
 </tool>