<?xml version="1.0"?>
<tool id="seqtk_mergepe" name="seqtk_mergepe" version="@TOOL_VERSION@.1">
    <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'
 #echo "| pigz --no-name --no-time" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
    ]]></command>
    <inputs>
        <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
        <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
    </inputs>
    <outputs>
        <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
    </outputs>
    <tests>
        <test>
            <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
            <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
            <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
        </test>
        <test>
            <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
            <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
            <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
        </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>
    <expand macro="citation" />
</tool>