# HG changeset patch
# User nml
# Date 1489600608 14400
# Node ID 624f99fe170588fab25a9fc9410537423025dd44
# Parent  7f59ee641f70a94029c69848688d00bc21bde237
planemo upload commit cf7305a207096e24bedddb0cb55bed86a6b7cd6b

diff -r 7f59ee641f70 -r 624f99fe1705 kat_sect.xml
--- a/kat_sect.xml	Mon Mar 13 15:53:39 2017 -0400
+++ b/kat_sect.xml	Wed Mar 15 13:56:48 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.1">
+<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
   <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description>
   <macros>
     <token name="@EXECUTABLE@">sect</token>
@@ -12,17 +12,17 @@
 
   cp "$db" db.fasta &&
   #if $single_or_paired.type == "single"
-    ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 
+    ln "$input_se" read.fastq && 
     kat sect 'db.fasta'
-    "$single_or_paired.input_se.element_identifier".fastq
+    read.fastq
   #elif $single_or_paired.type == "paired"
-    ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
+    ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
     kat sect 'db.fasta'
-    "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq
+    read_1.fastq read_2.fastq
   #else
-    ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
+    ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
     kat sect 'db.fasta'
-    "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
+    read_1.fastq read_2.fastq
   #end if  
 
   @THREADS@