<tool id="fastq_pair" name="Paired-end fastq pairer" profile="18.01" version="1.0+galaxy0">
    <description>Rewrite paired-end fastq files to make sure that all reads have a mate and to separate out singletons.</description>
    <requirements>
        <requirement type="package" version="1.0">fastq-pair</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

    ## Unzip gzipped inputs
    #if $fastq1.is_of_type("fastqsanger.gz"):
        gzip -d -c '$fastq1' > 1.fq &&
    #else:
        mv '$fastq1' 1.fq &&
    #end if

    #if $fastq2.is_of_type("fastqsanger.gz"):
        gzip -d -c '$fastq2' > 2.fq &&
    #else:
        mv '$fastq2' 2.fq &&
    #end if


    ## Run fastq_pair
    fastq_pair

    #if $table_size:
        -t '$table_size'
    #end if

    #if $print_elements:
        -p '$print_elements'
    #end if

    #if $verbose:
        '$verbose'
    #end if

    1.fq 2.fq

    ## Compress outputs
    #if $compress == "yes":
        ; gzip 1.fq.paired.fq
        ; gzip 2.fq.paired.fq
        ; gzip 1.fq.single.fq
        ; gzip 2.fq.single.fq
    #end if

    ]]></command>
    <inputs>
        <param name="verbose" label="Verbose" optional="true" value="false" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="true" help="Verbose output. This is mainly for debugging." />
        <param name="fastq1" label="FASTQ file 1" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 1 of pair" />
        <param name="fastq2" label="FASTQ file 2" type="data" format="fastqsanger,fastqsanger.gz" optional="false" help="FASTQ file input, file 2 of pair" />
        <param name="table_size" label="Table size" argument="-t" optional="true" value="100003" type="integer" help="Table size (default 100003)" />
        <param name="print_elements" label="Number elements to print" argument="-p" type="integer" optional="true" help="Print this number of elements in each bucket in the table." />
        <param name="compress" label="Compress outputs?" type="boolean" optional="true" value="true" truevalue="yes" falsevalue="no" checked="false" help="Check if outputs should be compressed (.gz)" />
    </inputs>
    <outputs>
        <collection name="uncompressed" type="list" format="fastqsanger" label="${tool.name} on ${on_string}: Paired reads and singletons">
            <filter>compress == False</filter>
                <data name="fwd_paired" from_work_dir="1.fq.paired.fq"/>
                <data name="rev_paired" from_work_dir="2.fq.paired.fq"/>
                <data name="fwd_single" from_work_dir="1.fq.single.fq"/>
                <data name="rev_single" from_work_dir="2.fq.single.fq"/>
        </collection>        
        <collection name="compressed" type="list" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Paired reads and singletons, compressed">
            <filter>compress</filter>
                <data name="fwd_paired_gz" from_work_dir="1.fq.paired.fq.gz"/>
                <data name="rev_paired_gz" from_work_dir="2.fq.paired.fq.gz"/>
                <data name="fwd_single_gz" from_work_dir="1.fq.single.fq.gz"/>
                <data name="rev_single_gz" from_work_dir="2.fq.single.fq.gz"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="table_size" value="1000"/>
            <param name="fastq1" value="left.fastq"/>
            <param name="fastq2" value="right.fastq"/>
            <output_collection name="uncompressed" type="list" count="4">
                <element name="fwd_paired" ftype="fastqsanger">
                    <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/1[ -~]+" /></assert_contents>
                </element>
                <element name="rev_paired" ftype="fastqsanger">
                    <assert_contents><has_line_matching expression="^@GFH7CG303GRT2I/2[ -~]+" /></assert_contents>
                </element>
                <element name="fwd_single" ftype="fastqsanger">
                    <assert_contents><has_line_matching expression="^@GFH7CG303GGIBL/1[ -~]+" /></assert_contents>
                </element>
                <element name="rev_single" ftype="fastqsanger">
                    <assert_contents><has_line_matching expression="^@GFH7CG303GSASH/2[ -~]+" /></assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="table_size" value="1000"/>
            <param name="fastq1" value="left.fastq.gz"/>
            <param name="fastq2" value="right.fastq.gz"/>
            <param name="compress" value="true"/>
            <output_collection name="compressed" type="list" count="4">
                <element name="fwd_paired_gz" ftype="fastqsanger.gz">
                    <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
                </element>
                <element name="rev_paired_gz" ftype="fastqsanger.gz">
                    <assert_contents><has_size value="16000" delta="1600"/></assert_contents>
                </element>
                <element name="fwd_single_gz" ftype="fastqsanger.gz">
                    <assert_contents><has_size value="62000" delta="6200"/></assert_contents>
                </element>
                <element name="rev_single_gz" ftype="fastqsanger.gz">
                    <assert_contents><has_size value="8500" delta="850"/></assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
=======================================================
Paired-end fastq pairer (fastq_pair)
=======================================================

Match up paired end fastq files quickly and efficiently. 
This galaxy tool can accept gzipped fastq files.

OPTIONS
-t table size (default 100003)
-p print the number of elements in each bucket in the table
-v verbose output. This is mainly for debugging
]]></help>
    <citations>
        <citation type="doi">10.1101/552885</citation>
    </citations>
</tool>