# HG changeset patch
# User cstrittmatter
# Date 1537181362 14400
# Node ID 8bafd3d18864eb1253d30d9dab64ce791d17eb41
# Parent  a368d48a4562f92f17349d87ebdaeda1f476775f
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

diff -r a368d48a4562 -r 8bafd3d18864 skesa.xml
--- a/skesa.xml	Thu Sep 13 09:34:22 2018 -0400
+++ b/skesa.xml	Mon Sep 17 06:49:22 2018 -0400
@@ -3,20 +3,25 @@
       <requirement type="package" version="2.2">skesa</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-    #if $jobtype.select != "cl"
+   
 	skesa
       #if $jobtype.select == "asm"
         --fasta $draft
       #else if $jobtype.select == "se"
-        --fastq $fastq1
+        --fastq $fastq
+      #else if $jobtype.select == "cl"
+        #set forward=$jobtype.coll.forward
+        #set reverse=$jobtype.coll.reverse
+	    --fastq $forward,$reverse --use_paired_ends
       #else if $jobtype.select == "pe"
-	    --fastq $fastq1,$fastq2 --use_paired_ends
+	    --fastq $forward,$reverse --use_paired_ends
+
       #end if
       #if $cores != 0
       --cores $cores
       #end if
       --memory $memory	> results.skesa.fasta
-    #end if 
+   
 
     ]]></command>
     <inputs>
@@ -25,16 +30,20 @@
           <option value="asm">Genome Assembly</option>
           <option value="se">Single-End Reads</option>
           <option value="pe">Paired-End Reads (Separate Files)</option>
+          <option value="cl">Paired collection from your history</option>
         </param>
         <when value="asm">
           <param name="draft" type="data" format="fasta" label="FASTA" />
         </when>
         <when value="se">
-          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
+        </when>
+        <when value="cl">
+          <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
         </when>
         <when value="pe">
-          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
-          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+          <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
+          <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" />
         </when>
       </conditional>
       <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />