# HG changeset patch
# User sanbi-uwc
# Date 1552071310 18000
# Node ID 72cb19a32d8b01a7b485ff22f58f000cace9d9b9
# Parent  2cde7c81c694f14790581189d2a1d6678a58da9e
planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty

diff -r 2cde7c81c694 -r 72cb19a32d8b confil.xml
--- a/confil.xml	Fri Mar 08 12:46:23 2019 -0500
+++ b/confil.xml	Fri Mar 08 13:55:10 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy3">
+<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy4">
     <macros>
         <token name="@VERSION@">0.1.3</token>
     </macros>
@@ -19,9 +19,9 @@
         if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff 
           $input_type_conditional.single_input.element_identifier ;
         then 
-          ln -sf "${input_type_conditional.single_input}" '$single_output_file'
+          ln -sf "${input_type_conditional.single_input}" '$single_output_file' ;
 	else
-	  touch '$single_output_file'  # failure - make empty file
+	  touch '$single_output_file' ;
 	fi
         ####### Paired Collection
         #elif $input_type == "paired_collection"
@@ -34,9 +34,9 @@
         $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier ;
 	then 
           ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward'
-          && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse'
+          && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse' ;
 	else
-	  touch '$list_output.forward' && touch '$list_output.reverse'  # failure - make empty files
+	  touch '$list_output.forward' && touch '$list_output.reverse' ;
 	fi
         #end if
         && mv $report_name '$output_report'