--- a/trim_galore.xml	Thu Apr 20 09:14:30 2017 -0400
+++ b/trim_galore.xml	Mon Apr 24 14:30:07 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
-    <!-- Wrapper compatible with Trim Galore! version 0.4 -->
+<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01">
+    <!-- Wrapper compatible with Trim Galore! version 0.4.3 -->
     <description>Quality and adapter trimmer of reads</description>
     <macros>
         <macro name="adapter_trimming">
@@ -24,7 +24,6 @@
             </conditional>
         </macro>
         <macro name="paired_adapter_trimming">
-
             <expand macro="adapter_trimming">
                 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
                     <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
@@ -44,16 +43,12 @@
         </macro>
     </macros>
     <requirements>
-        <!-- conda dependency -->
-        <requirement type="package" version="1.8.3">cutadapt</requirement>
-        <requirement type="package" version="1.8">cutadapt</requirement>
+        <requirement type="package" version="0.4.3">trim-galore</requirement>
     </requirements>
     <version_command>
-        perl '$__tool_directory__/trim_galore' --version
+        trim_galore --version
     </version_command>
-    <command>
-<![CDATA[
-
+    <command><![CDATA[
         #set compressed = 'no'
         #if $singlePaired.sPaired == "single":
             #if $singlePaired.input_singles.is_of_type("fastq.gz"):
@@ -95,7 +90,7 @@
             ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
         #end if
 
-        perl '$__tool_directory__/trim_galore'
+        trim_galore
 
         ## we only support fastqsanger
         --phred33
@@ -146,13 +141,12 @@
         #if $singlePaired.trimming.trimming_select == 'user':
             ## default 'AGATCGGAAGAGC'
             #if $singlePaired.trimming.adapter.strip() != '':
-               --adapter $singlePaired.trimming.adapter
+               --adapter '$singlePaired.trimming.adapter'
             #end if
         #else:
             $singlePaired.trimming.trimming_select
         #end if
 
-
         #if $singlePaired.three_prime_clip_R1:
             --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
         #end if
@@ -167,7 +161,7 @@
 
             #if $singlePaired.trimming.trimming_select == 'user':
                 #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '':
-                    --adapter2 $singlePaired.trimming.adapter2
+                    --adapter2 '$singlePaired.trimming.adapter2'
                 #end if
             #end if
 
@@ -199,11 +193,9 @@
         ##  Trim Galore! run is finished. Move the report files to the proper place
         #if $params.settingsType == "custom" and $params.report:
             &&
-            cat ./*_trimming_report.txt > $report_file;
+            cat ./*_trimming_report.txt > '$report_file'
         #end if
-
-]]>
-    </command>
+    ]]></command>
     <inputs>
         <!-- Input Parameters -->
         <conditional name="singlePaired">
@@ -283,8 +275,8 @@
                     label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" />
             </when>  <!-- full -->
         </conditional>  <!-- params -->
+    </inputs>
 
-    </inputs>
     <outputs>
         <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
             <filter>singlePaired['sPaired'] == "single"</filter>
@@ -331,8 +323,8 @@
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['report'] == True</filter>
         </data>
+    </outputs>
 
-    </outputs>
     <tests>
         <test>
             <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
@@ -449,8 +441,7 @@
             </output_collection>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 `Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are:
@@ -473,7 +464,7 @@
 * **Adapter sequence to be trimmed**
 
   * **Automatic detection**
-    
+
       | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used.
 
   * **Illumina universal**
@@ -518,7 +509,7 @@
       |   R2 <---------------------------
       |
       | or this:
-      | 
+      |
       |   R1 ----------------------->
       |   R2 <-----------------
       |
@@ -600,7 +591,7 @@
 
     | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well.
     |
-    | *option --non_directional*]]>
-    </help>
+    | *option --non_directional*
+    ]]></help>
     <citations></citations>
 </tool>