# HG changeset patch
# User sanbi-uwc
# Date 1550136974 18000
# Node ID ca3c6f955c3e065b2aa4471c9ca13eb61511997a
# Parent  d5b37a19547a8aa693a49c1ff64955286aa71a9c
planemo upload for repository https://github.com/COMBAT-TB/confil commit 692db20f6abdd864953054c4c8c43d5192a87e3d

diff -r d5b37a19547a -r ca3c6f955c3e confil.xml
--- a/confil.xml	Wed Feb 13 09:02:41 2019 -0500
+++ b/confil.xml	Thu Feb 14 04:36:14 2019 -0500
@@ -3,16 +3,29 @@
         <requirement type="package" version="7.0">click</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        confil --threads $threads
         #set $input_type = $input_type_conditional.input_type
-        #if $input_type == "paired_collection"
-        --paired 
-        #end if
-        --cutoff $cutoff 
+        #import re
+
+        ####### Single Input
         #if $input_type == "single"
-        "${input_type_conditional.single_input}"
+        ln -s "${input_type_conditional.single_input}" $input_type_conditional.single_input.element_identifier &&
+        #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0]
+        #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab'
+
+        confil --threads $threads --cutoff $cutoff 
+        $input_type_conditional.single_input.element_identifier
+        && mv $report_name '$output'
+
+        ####### Paired Collection
         #elif $input_type == "paired_collection"
-        "${input_type_conditional.collection_input.forward}" "${input_type_conditional.collection_input.reverse}"
+        ln -s "${input_type_conditional.collection_input.forward}" $input_type_conditional.collection_input.forward.element_identifier &&
+        ln -s "${input_type_conditional.collection_input.reverse}" $input_type_conditional.collection_input.reverse.element_identifier &&
+        #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0]
+        #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab'
+
+        confil --threads $threads --cutoff $cutoff --paired 
+        $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier
+        && mv $report_name '$output'
         #end if
     ]]>
     </command>