diff seqtk_listhet.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_listhet.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,47 @@
+<?xml version="1.0"?>
+<tool id="seqtk_listhet" name="seqtk_listhet" version="@WRAPPER_VERSION@.0">
+  <description>extract the position of each het</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk listhet $in_file  | awk 'BEGIN{print "#chr\tposition\tbase"}1' > $default]]></command>
+  <inputs>
+    <expand macro="in_faq"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" hidden="false" name="default" label="Positions of heterozygous bases in $in_file.name"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_file" value="seqtk_listhet.fa"/>
+      <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Lists regions of heterozygosity.
+
+::
+
+    >ambig
+    ACGTMRWSYKVHDBN
+
+The seqtk suite recognises MRWSYK:
+
+::
+
+    #chr    position  base
+    ambig   5         M
+    ambig   6         R
+    ambig   7         W
+    ambig   8         S
+    ambig   9         Y
+    ambig   10        K
+
+
+@ATTRIBUTION@
+]]></help>
+</tool>