# HG changeset patch
# User jowong
# Date 1542888155 18000
# Node ID 1850de9baad05e296da930220e1282bae7b65323
# Parent  aaeba1765ceb8afff58ec6e3482e73b89519ef04
planemo upload

diff -r aaeba1765ceb -r 1850de9baad0 kwip.xml
--- a/kwip.xml	Mon Nov 19 09:35:55 2018 -0500
+++ b/kwip.xml	Thu Nov 22 07:02:35 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="kwip" name="kwip" version="1.1.5">
-    <description>Calculates CNV of genomic data based on template</description>
+<tool id="kwip" name="kwip" version="1.1.6">
+    <description>Calculates k-mer weighted inner product, a de novo estimator of genetic similarity</description>
     <requirements>
         <requirement type="package" version="0.2.0">kwip</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        #for $input in $inputs# cp $input "$input.element_identifier".ct.gz && #end for# 
+        #for $input in $inputs# cp $input $(basename "$input.element_identifier" .fastq).ct.gz && #end for# 
         kwip 
         -t $advanced.thread 
         -k kwip.kernel 
@@ -13,7 +13,8 @@
         #if str( $advanced.calc ) == "True"
             -w $advanced.weight -C
         #end if 
-        #for $input in $inputs# "$input.element_identifier".ct.gz #end for#
+        #for $input in $inputs# $(basename "$input.element_identifier" .fastq).ct.gz #end for#
+	#for $input in $inputs# && rm $(basename "$input.element_identifier" .fastq).ct.gz  #end for#
     ]]></command>
     <inputs>
         <param name="inputs" format="data" type="data_collection" label="inputs" help="Specify dataset with hashed reads"/>
@@ -26,8 +27,8 @@
         </section>
     </inputs>
     <outputs>
-        <data name="kwip_kernel" label="kWip kernel" format="data" from_work_dir="kwip.kernel"/>
-        <data name="kwip_distance" label="kWip distance" format="data" from_work_dir="kwip.dist"/>
+        <data name="kwip_kernel" label="kWip kernel" format="txt" type="data" from_work_dir="kwip.kernel"/>
+        <data name="kwip_distance" label="kWip distance" format="txt" type="data" from_work_dir="kwip.dist"/>
     </outputs>
     <tests>
     </tests>