<?xml version="1.0"?>
<tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
  <description>cut sequence at long N</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk cutN -n $n
-p $p
$g
$in_file
> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
    <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
    <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
    <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
  </inputs>
  <outputs>
    <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
  </outputs>
  <tests>
    <test>
      <param name="in_file" value="seqtk_cutn.fa"/>
      <param name="n" value="1"/>
      <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Splits long sequences with runs of Ns

::

    >test
    AACTGATCGATCGATCGNNNNNNNNNNNACATG

This will be split into the component sequences without the ambiguity.

::

    >test:1-17
    AACTGATCGATCGATCG
    >test:29-33
    ACATG


@ATTRIBUTION@
      ]]></help>
</tool>