# HG changeset patch
# User bgruening
# Date 1453715073 18000
# Node ID 8352713cf9397d980b49c20bd97f7f6e186f5f5e
# Parent  11962ce408556fa9c4607dd0009c995af5fe1ef0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 07148c518916e16602ea26473d00358fe04bc3b6-dirty

diff -r 11962ce40855 -r 8352713cf939 trim_galore.xml
--- a/trim_galore.xml	Wed Oct 07 08:39:59 2015 -0400
+++ b/trim_galore.xml	Mon Jan 25 04:44:33 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="trim_galore" name="Trim Galore!" version="0.4.0">
+<tool id="trim_galore" name="Trim Galore!" version="0.4.1">
     <!-- Wrapper compatible with Trim Galore! version 0.4 -->
     <description>adaptive quality and adapter trimmer</description>
     <macros>
@@ -11,7 +11,7 @@
                     <option value="--small_rna">Illumina small RNA adapters</option>
                     <option value="user">User defined adapter trimming</option>
                 </param>
-                <when value="auto"/>
+                <when value=""/>
                 <when value="--illumina"/>
                 <when value="--nextera"/>
                 <when value="--small_rna"/>
@@ -269,14 +269,14 @@
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq"
+        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
             label="${tool.name} on ${on_string}: unpaired reads (1)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq"
+        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
             label="${tool.name} on ${on_string}: unpaired reads (2)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>