<?xml version="1.0"?>
<tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
  <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk mergepe
      $in_fq1
      $in_fq2
> $default]]></command>
  <inputs>
    <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
    <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
  </inputs>
  <outputs>
      <data format_source="in_fq1" hidden="false" name="default" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
  </outputs>
  <tests>
    <test>
      <param name="in_fq1" value="paired_dat1.fq"/>
      <param name="in_fq2" value="paired_dat2.fq"/>
      <output name="default" file="paired_dat.fq" ftype="fastq"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file

::

    # r1.fq
    @test-6/1
    AGCTTGACGC
    +
    ?.HCF@C>>F

    # r2.fq
    @test-6/2
    TGCGAAGACC
    +
    >2?A?A@@7?

will produce the following paired file:

::

    @test-6/1
    AGCTTGACGC
    +
    ?.HCF@C>>F
    @test-6/2
    TGCGAAGACC
    +
    >2?A?A@@7?

While this may not have been an illuminating example, it is important to note
that this tool will properly interleave data. For example if you have the ids:

::

    @r-1/1
    @r-2/1
    @r-3/1
    @r-4/1

and

::

    @r-1/2
    @r-2/2
    @r-3/2
    @r-4/2

These will be interleaved as

::

    @r-1/1
    @r-1/2
    @r-2/1
    @r-2/2
    @r-3/1
    @r-3/2
    @r-4/1
    @r-4/2

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