Mercurial > repos > mgarnier > pangenome_cog_analysis

changeset 7:3f4e4e7d77ff draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mgarnier
date Fri, 02 Jul 2021 19:25:36 +0000
parents cf9da93e4145
children 9132bdc6ce8b
files pangenomeCogAnalysis.xml
diffstat 1 files changed, 3 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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>