# HG changeset patch
# User estrain
# Date 1534441106 14400
# Node ID f9b8095f18fee6e33af409cdac1ca3caf27057a2
# Parent  b82a1b3c5b61281124798f00c9ef400cb0cae403
Uploaded

diff -r b82a1b3c5b61 -r f9b8095f18fe skesa.xml
--- a/skesa.xml	Wed Aug 15 17:35:46 2018 -0400
+++ b/skesa.xml	Thu Aug 16 13:38:26 2018 -0400
@@ -13,6 +13,8 @@
         --fastq $fastq1
       #else if $jobtype.select == "pe"
 	--fastq $fastq1,$fastq2 --use_paired_ends
+      #else if $jobtype.select == "pe"
+	--fastq $pairedfiles.forward,$pairedfiles.reverse --use_paired_ends
       #end if
       #if $cores != 0
       --cores $cores
@@ -30,7 +32,8 @@
           <option value="sra">SRR  number</option>
           <option value="asm">Genome Assembly</option>
           <option value="se">Single-End Reads</option>
-          <option value="pe">Paired-End Reads</option>
+          <option value="pe">Paired-End Reads (Separate Files)</option>
+          <option value="rp">Paired-End Reads (Paired Data Set)</option>
           <option value="cl">Collection of Reads</option>
         </param>
         <when value="asm">
@@ -46,6 +49,9 @@
          <when value="cl">
               <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
         </when>
+         <when value="rp">
+              <param type="data_collection" name="pairedfiles" format="fastq" collection_type="paired" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
+        </when>
       </conditional>
       <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
       <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />