--- a/sortmerna.xml	Wed Dec 09 09:21:28 2015 -0500
+++ b/sortmerna.xml	Tue Mar 29 06:53:28 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1.0">
+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0">
     <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
     <requirements>
-        <requirement type='package' version="2.0">sortmerna</requirement>
+        <requirement type="package" version="2.1b">sortmerna</requirement>
     </requirements>
     <stdio>
         <regex match="This program builds a Burst trie on an input rRNA database"
@@ -12,6 +12,10 @@
             source="both"
             level="fatal"
             description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
+        <regex match="ERROR"
+            source="both"
+            level="fatal"
+            description="ERROR" />
     </stdio>
     <version_command>
 <![CDATA[
@@ -76,9 +80,7 @@
     	$log
 
         #if $report.report_type == 'best'
-            #if $report.report_best.report_best_type == '0'
-                --best 0
-            #else if $report.report_best.report_best_type == '1'
+            #if $report.report_best.report_best_type == '1'
                 --best 1
                 --min_lis $report.report_best.report_best_min_lis
             #else
@@ -195,11 +197,9 @@
             <when value="best">
                 <conditional name="report_best">
                     <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
-                        <option value="0">All high-candidate reference sequences are searched for alignments (very slow)</option>
                         <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
                         <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
                     </param>
-                    <when value="0" />
                     <when value="1">
                         <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
                     </when>