--- a/seqtk_trimfq.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_trimfq.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,63 +1,65 @@
 <?xml version="1.0"?>
 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
-  <description>trim FASTQ using the Phred algorithm</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk trimfq
+    <description>trim FASTQ using the Phred algorithm</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk trimfq
 #if $mode.mode_select == "quality":
--q $mode.q
--l $mode.l
+    -q $mode.q
+    -l $mode.l
 #else:
--b $mode.b
--e $mode.e
+    -b $mode.b
+    -e $mode.e
 #end if
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <conditional name="mode">
-        <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
-            <option value="quality">Quality</option>
-            <option value="position">Length/Position</option>
-        </param>
-        <when value="quality">
-            <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/>
-            <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/>
-        </when>
-        <when value="position">
-            <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/>
-            <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/>
-        </when>
-    </conditional>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_trimfq.fq"/>
-      <param name="mode_select" value="quality"/>
-      <param name="q" value="0.05"/>
-      <param name="l" value="30"/>
-      <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
-    </test>
-    <test>
-      <param name="in_file" value="seqtk_trimfq.fq"/>
-      <param name="mode_select" value="position"/>
-      <param name="b" value="5"/>
-      <param name="e" value="5"/>
-      <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <conditional name="mode">
+            <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
+                <option value="quality">Quality</option>
+                <option value="position">Length/Position</option>
+            </param>
+            <when value="quality">
+                <param argument="-q" type="float" value="0.05" label="Error rate threshold" />
+                <param argument="-l" type="integer" value="30" label="Maximally trim down to INT bp" />
+            </when>
+            <when value="position">
+                <param argument="-b" type="integer" value="0" label="Trim INT bp from left" />
+                <param argument="-e" type="integer" value="0" label="Trim INT bp from right" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" label="$in_file.name trimmed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_trimfq.fq"/>
+            <param name="mode_select" value="quality"/>
+            <param name="q" value="0.05"/>
+            <param name="l" value="30"/>
+            <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_trimfq.fq"/>
+            <param name="mode_select" value="position"/>
+            <param name="b" value="5"/>
+            <param name="e" value="5"/>
+            <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Trim a fastq file based on Phred scores, or by length
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>