--- a/seqtk_sample.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_sample.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,39 +1,42 @@
 <?xml version="1.0"?>
 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
     <description>random subsample of fasta or fastq sequences</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk sample -s $s
-      $in_file
-      $subsample_size
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq" />
-    <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
-    <param label="Subsample (decimal fraction or number)" name="subsample_size" type="float" value="100"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_sample.fa"/>
-      <param name="subsample_size" value="4"/>
-      <param name="s" value="4"/>
-      <output name="default" file="seqtk_sample.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk sample
+-s $s
+'$in_file'
+$subsample_size
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq" />
+        <param argument="-s" type="integer" value="4" label="RNG seed" help="The seed used for the random number generator. Manually specifying a number here is useful for reproducing the same subsampling over time" />
+        <param name="subsample_size" type="float" value="100" label="Subsample (decimal fraction or number)" />
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" label="Subsample of reads from $in_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_sample.fa"/>
+            <param name="subsample_size" value="4"/>
+            <param name="s" value="4"/>
+            <output name="default" file="seqtk_sample.out" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
-Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
+Takes a random subsample of FASTA or FASTQ sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__.
 
 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset.
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>