--- a/seqtk_seq.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_seq.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,22 +1,23 @@
 <?xml version="1.0"?>
-<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0">
-  <description>common transformation of FASTA/Q</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk seq -q $q
+<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.2">
+    <description>common transformation of FASTA/Q</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk seq -q $q
 -X $X
-#if $n and $n != "None" and $n is not None and $n != "":
--n "$n"
+#if $n:
+    -n '$n'
 #end if
 -l $l
 -Q $Q
 -s $s
 -f $f
-#if $M and $M != "None" and $M is not None and $M != "":
--M "$M"
+#if $M:
+    -M '$M'
 #end if
 -L $L
 $c
@@ -26,53 +27,52 @@
 $N
 $x1
 $x2
-#if $in_file.ext == "fastqillumina"
- -V
+#if $in_file.is_of_type('fastqillumina')
+    -V
 #end if
-
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/>
-    <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/>
-    <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/>
-    <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/>
-    <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/>
-    <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/>
-    <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/>
-    <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/>
-    <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/>
-    <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/>
-    <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
-    <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/>
-    <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/>
-    <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
-    <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
-    <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default"/>
-  </outputs>
-  <tests>
-    <test>
-      <!-- This is a sorry excuse for a test for a tool which does way more
-           than it should, but upstream decided to put a TON of functionality
-           into a single tool rather than using the single responsibility
-           principle. -->
-      <param name="in_file" value="seqtk_seq.fa"/>
-      <param name="r" value="True"/>
-      <param name="n" value=""/>
-      <param name="M" value=""/>
-      <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
+        <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
+        <param argument="-n" type="text" value="0" label="Masked bases converted to CHAR; 0 for lowercase" />
+        <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
+        <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" />
+        <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
+        <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
+        <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
+        <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
+        <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
+        <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Reverse complement" />
+        <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
+        <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
+        <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
+        <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
+        <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" />
+    </outputs>
+    <tests>
+        <!-- This is a sorry excuse for a test for a tool which does way more
+             than it should, but upstream decided to put a TON of functionality
+             into a single tool rather than using the single responsibility
+             principle. -->
+        <test>
+            <param name="in_file" value="seqtk_seq.fa"/>
+            <param name="r" value="True"/>
+            <param name="n" value=""/>
+            <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Various utilities for transforming FASTA/Q data
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>