--- a/seqtk_subseq.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_subseq.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,60 +1,60 @@
 <?xml version="1.0"?>
 <tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
-  <description>extract subsequences from FASTA/Q files</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk subseq $t
+    <description>extract subsequences from FASTA/Q files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk subseq
+$t
 -l $l
-$in_file
-
+'$in_file'
 #if $source.type == 'bed':
-  $in_bed
+    '$in_bed'
 #else
-  $name_list
+    '$name_list'
 #end if
-
 #if $t == '-t':
- | awk 'BEGIN{print "chr\tunknown\tseq"}1'
+    | awk 'BEGIN{print "chr\tunknown\tseq"}1'
 #end if
-
-> $default]]></command>
-  <inputs>
-    <param name="in_file" type="data" format="fasta,fastq" label="Input fasta/q file"/>
-    <conditional name="source">
-      <param name="type" type="select" label="Select source of sequence choices">
-        <option value="bed">BED</option>
-        <option value="name">FASTA/Q ID list</option>
-      </param>
-      <when value="bed">
-        <param name="in_bed" type="data" format="bed" label="Input BED file"/>
-      </when>
-      <when value="name">
-        <param name="name_list" type="data" format="txt" label="Input fasta file"/>
-      </when>
-    </conditional>
-    <param label="TAB delimited output" help="(-t)" name="t" type="boolean" falsevalue="" truevalue="-t"/>
-    <param label="sequence line length" help="(-l)" name="l" type="integer" value="0"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Selected sequences from $in_file.name">
-      <change_format>
-        <when input="t" value="-t" format="tabular"/>
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_subseq.fa"/>
-      <param name="type" value="name"/>
-      <param name="t" value="False" />
-      <param name="name_list" value="seqtk_subseq_list.txt"/>
-      <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <conditional name="source">
+            <param name="type" type="select" label="Select source of sequence choices">
+                <option value="bed">BED</option>
+                <option value="name">FASTA/Q ID list</option>
+            </param>
+            <when value="bed">
+                <param name="in_bed" type="data" format="bed" label="Input BED file"/>
+            </when>
+            <when value="name">
+                <param name="name_list" type="data" format="txt" label="Input ID list"/>
+            </when>
+        </conditional>
+        <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
+        <param argument="-l" type="integer" value="0" label="Sequence line length" />
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
+            <change_format>
+                <when input="t" value="-t" format="tabular"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_subseq.fa"/>
+            <param name="type" value="name"/>
+            <param name="t" value="False" />
+            <param name="name_list" value="seqtk_subseq_list.txt"/>
+            <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
@@ -79,6 +79,6 @@
     ACGTMRWSYK
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>