<tool id="b2b_sync_reads" name="Sync paired reads"
    version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="21.01">

    <description>Synchronize trimmed/filtered read-pair set</description>
    <macros>
        <token name="@TOOL_NAME@">sync_reads</token>
        <token name="@TOOL_VERSION@">0.005</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="version_command" />

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

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

    sync_reads
    --fwd $input1
    --rev $input2
    --fwd_out $fwd_out
    --rev_out $rev_out
    #if str($write_singles) == 'y':
	--singles
        --fwd_singles_out $fwd_s_out
        --rev_singles_out $rev_s_out
    #end if

    ]]>
    </command>

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

    <inputs>

        <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
          help="Only letters, numbers and underscores (_) will be retained in this field">
           <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"><add value="_" /> </valid>
           </sanitizer>
        </param>
        <!-- FASTQ input(s) and options specifically for paired-end data. -->
        <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
        <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
        <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />

    </inputs>

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

    <outputs>
        <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
        <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
        <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
            <filter>write_singles</filter>
        </data>
        <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
            <filter>write_singles</filter>
        </data>
    </outputs>

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

    <tests>

        <test expect_num_outputs="2">
            <param name="input1" value="test_R1.fq" ftype="fastq" />
            <param name="input2" value="test_R2.fq" ftype="fastq" />
            <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
            <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
        </test>

        <test expect_num_outputs="4">
            <param name="input1" value="test_R1.fq" ftype="fastq" />
            <param name="input2" value="test_R2.fq" ftype="fastq" />
            <param name="write_singles" value="True" />
            <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
            <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
            <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
            <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
        </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>