<?xml version="1.0"?>
<tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
  <description>drop unpaired from interleaved Paired End FASTA/Q</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk dropse
      $in_file
> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
  </inputs>
  <outputs>
    <data format_source="in_file" hidden="false" name="default" label="Only paired-end reads from $in_file.name"/>
  </outputs>
  <tests>
    <test>
      <param name="in_file" value="seqtk_dropse.fq"/>
      <output name="default" file="seqtk_dropse.out" ftype="fastq"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:

::

    @test-6/1
    AGCTTGACGC
    +
    ?.HCF@C>>F
    @test-6/2
    TGCGAAGACC
    +
    >2?A?A@@7?
    @test-4/1
    CTTGACGCTG
    +
    I@>3EFCG@C
    @test-2/1
    AGACCAAAAT
    +
    ??><6E?IFC
    @test-2/2
    CTGGCGAATT
    +
    ?=?*?A?<?@

This tool will remove the offending reads (test-4/1), leaving just the paired data.

::

    @test-6/1
    AGCTTGACGC
    +
    ?.HCF@C>>F
    @test-6/2
    TGCGAAGACC
    +
    >2?A?A@@7?
    @test-2/1
    AGACCAAAAT
    +
    ??><6E?IFC
    @test-2/2
    CTGGCGAATT
    +
    ?=?*?A?<?@


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