# HG changeset patch
# User bebatut
# Date 1446035355 14400
# Node ID 5d7ec21f6d4cd3c4d3717c6cee0dd11f41e975f8
# Parent  9c19086ae6264a74d6cd691270cf8ce71060ee5a
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty

diff -r 9c19086ae626 -r 5d7ec21f6d4c sortmerna.xml
--- a/sortmerna.xml	Wed Oct 28 08:23:45 2015 -0400
+++ b/sortmerna.xml	Wed Oct 28 08:29:15 2015 -0400
@@ -51,17 +51,15 @@
         #end if
 
         #if $sam.test:
-            --aligned $sam_alignment_file
             --sam
             $sam.sq_tag
         #end if
 
         #if $blast.test:
-            --aligned $blast_output_file
             --blast "$blast.format"
         #end if
 
-        $log.test
+        $log
 
         #if $report.type == 'best':
             #if $report.best.type == '0':
@@ -146,9 +144,7 @@
             </when>
         </conditional>
 
-        <conditional name="log">
-            <param name='test' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
-        </conditional>
+        <param name='log' type='boolean' checked="true" truevalue='--log' falsevalue='' label="Conserve overall statistic output into a log file?" help=""/>
 
         <conditional name="report">
             <param name="type" type="select" display="radio" label="Parameters for filtering and read mapping" help="">
@@ -223,7 +219,7 @@
         </data>
 
         <data format="txt" name="output_log" metadata="input_sequence_file" from_work_dir="aligned.log">
-            <filter>log.test</filter>
+            <filter>log</filter>
         </data>
     </outputs>