view seqtk_listhet.xml @ 1:61718851f199 draft

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<?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>