<tool id="b2b_@TOOL_NAME@" name="Interleave reads"
    version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
    <description>Interleaved paired FASTQ files</description>
    <macros>
        <token name="@TOOL_NAME@">fq_interleave</token>
        <token name="@TOOL_VERSION@">0.202</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
    </edam_operations>
    <expand macro="requirements">
        <expand macro="requirement_pigz" />
    </expand>
    <expand macro="version_command" />

    <!-- ***************************************************************** -->

    <command detect_errors="aggressive" strict="true">
    <![CDATA[

    set -o pipefail;

    fq_interleave
    --1 $input1
    --2 $input2
    $check
    $rename
    $compress_output
    > $output

    ]]>
    </command>

    <!-- ***************************************************************** -->

    <inputs>
        <param name="input1"
            type="data"
            format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
            label="Forward reads"
            help="Forward read FASTQ file" />
        <param name="input2"
            type="data"
            format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
            label="Reverse reads"
            help="Reverse read FASTQ file" />
        <param argument="--check"
            type="boolean"
            label="Check names"
            checked="False"
            truevalue="--check"
            falsevalue=""
            help="Verify that paired names match" />
        <param argument="--rename"
            type="boolean"
            label="Rename"
            checked="False"
            truevalue="--rename"
            falsevalue=""
            help="Ensure /1 and /2 at end of read names" />
        <param name="compress_output"
            type="boolean"
            checked="true"
            truevalue="@PIPE_PIGZ@"
            falsevalue=""
            label="Compress output" />
    </inputs>

    <!-- ***************************************************************** -->

    <outputs>
        <data name="output" format="fastq.gz">
            <change_format>
                <when input="compress_output" value="" format="fastq" />
            </change_format>
        </data>
    </outputs>

    <!-- ***************************************************************** -->

    <tests>

        <!-- default options -->
        <test expect_num_outputs="1">
            <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
            <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
            <output name="output" file="test.il.fq" compare="diff" ftype="fastq.gz" decompress="true"/>
            <assert_command>
                <not_has_text text="--check " />
                <not_has_text text="--rename " />
            </assert_command>
        </test>
        <!-- mismatched inputs -->
        <test expect_failure="true">
            <param name="input1" value="test_R1.fq" ftype="fastq" />
            <param name="input2" value="test_R2.fq" ftype="fastq" />
            <param name="check" value="true" />
        </test>
        <!-- other options -->
        <test expect_num_outputs="1">
            <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
            <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
            <param name="check" value="true" />
            <param name="rename" value="true" />
            <param name="compress_output" value="false" />
            <output name="output" file="test.il.fq" compare="diff" ftype="fastq" />
            <assert_command>
                <has_text text="--check" />
                <has_text text="--rename" />
            </assert_command>
        </test>

    </tests>

    <!-- ***************************************************************** -->

    <help>

    sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
    reverse FASTQ read files. It will output a new pair of files containing only
    read pairs found in both input files. It can optionally output singletons from
    each input file as well.

    </help>

    <!-- ***************************************************************** -->

    <citations>
    </citations>

</tool>