<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>on paired end reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3359</edam_operation>
    </edam_operations>
    <expand macro="requirements"/>
    <command><![CDATA[
gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
    </inputs>
    <outputs>
        <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
        <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
        <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
        <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
            <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
            <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
            <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
            <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
            <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
            <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_file" value="paired_end_merged_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
            <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
            <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
        </test>
        <test>
            <param name="input_file" value="paired_end_merged_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
            <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
            <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
            <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
            <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.

Sequence identifiers for paired-end reads must follow the /1 and /2 convention.

-----

**Input**

A multiple-fastq file containing paired-end reads, for example::

    @1539:931/1
    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
    +1539:931/1
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    @1539:931/2
    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
    +1539:931/2
    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

-----

**Output**

Multi-fastq file with left-hand mate only::

    @1539:931/1
    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
    +1539:931/1
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

Multi-fastq file with right-hand mate only::

    @1539:931/2
    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
    +1539:931/2
    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>