<?xml version="1.0"?>
<tool id="seqtk_dropse" name="seqtk_dropse" version="@TOOL_VERSION@.1">
    <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'
@CONDITIONAL_GZIP_OUT@
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" label="Only paired-end reads from $in_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_dropse.fq" ftype="fastqsanger"/>
            <output name="default" file="seqtk_dropse.out" ftype="fastqsanger"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_dropse.fq.gz" ftype="fastqsanger.gz"/>
            <output name="default" file="seqtk_dropse.out.gz" ftype="fastqsanger.gz"/>
        </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>
    <expand macro="citation" />
</tool>