--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_subseq.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,83 @@
+<?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
+-l $l
+$in_file
+
+#if $source.type == 'bed':
+  $in_bed
+#else
+  $name_list
+#end if
+
+#if $t == '-t':
+ | 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[
+**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.
+
+::
+
+    # Input ID list
+    seq1
+
+    # Input fasta
+    >seq1
+    ACGTMRWSYK
+    >seq2
+    RWSYKACGTM
+
+results in
+
+::
+
+    # Output result
+    >seq1
+    ACGTMRWSYK
+
+@ATTRIBUTION@
+]]></help>
+</tool>