# HG changeset patch
# User rnateam
# Date 1494512813 14400
# Node ID e1c5ca2a4562a6c6496c3dd42ab615af2bb631f9
# Parent  bf2866308fbd25cc76b73b05355ff9573d3b8fb0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit b'eebcbcf7ec7804eb97e6be0f417d01fd3422ab32\n'

diff -r bf2866308fbd -r e1c5ca2a4562 sortmerna.xml
--- a/sortmerna.xml	Wed Jun 15 05:31:10 2016 -0400
+++ b/sortmerna.xml	Thu May 11 10:26:53 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.1">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.2">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
     <requirements>
         <requirement type="package" version="2.1b">sortmerna</requirement>
@@ -117,8 +117,8 @@
             <when value="paired">
                 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
                     <option value="">leave the reads split between aligned and rejected files</option>
-                    <option value="--paired-in">output both reads to aligned file (--paired-in)</option>
-                    <option value="--paired-out">output both reads to rejected file (--paired-out)</option>
+                    <option value="--paired_in">output both reads to aligned file (--paired_in)</option>
+                    <option value="--paired_out">output both reads to rejected file (--paired_out)</option>
                 </param>
             </when>
         </conditional>