<tool id="b2b_summarize_run" name="Summarize run" version="0.002">

    <description>Summarize sequencing run and assembly statistics</description>

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

    <requirements>
    <!--
        <requirement type="package" version="0.003">b2b-utils</requirement>
    -->
        <requirement type="package" version="0.7.17">bwa</requirement>
        <requirement type="package" version="0.008009">perl-biox-seq</requirement>
        <requirement type="package" version="1.23">perl-file-which</requirement>
    </requirements>

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

    <version_command>echo "0.002"</version_command>

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

    <command detect_errors="aggressive">
    <![CDATA[
    perl $__tool_directory__/frag_lens
        --forward "$in_filt1"
        --reverse "$in_filt2"
        --ref "$in_ref"
        --threads  "\${GALAXY_SLOTS:-1}"
        --max_aln 100000
    | perl $__tool_directory__/summarize_run.pl
        --raw_1     $in_raw1
        --raw_2     $in_raw2
        --filt_1    $in_filt1
        --filt_2    $in_filt2
        --consensus $in_ref
        --bedgraph  $in_bg
        --fastqc_1  $in_fqc1
        --fastqc_2  $in_fqc2
        --out       $report
        --threads   "\${GALAXY_SLOTS:-1}"
    ;

    ]]>
    </command>

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

    <inputs>
	    <param format="fastqsanger,fastq" name="in_raw1" type="data" label="Raw forward reads" />
	    <param format="fastqsanger,fastq" name="in_raw2" type="data" label="Raw reverse reads" />
	    <param format="fastqsanger,fastq" name="in_filt1" type="data" label="Filtered/synced forward reads" />
	    <param format="fastqsanger,fastq" name="in_filt2" type="data" label="Filtered/synced reverse reads" />
	    <param format="fasta" name="in_ref" type="data" label="Consensus (FASTA)" />
	    <param format="bedgraph" name="in_bg" type="data" label="Coverage (bedgraph)" />
	    <param format="txt" name="in_fqc1" type="data" label="Raw FastQC (forward reads)" />
	    <param format="txt" name="in_fqc2" type="data" label="Raw FastQC (reverse reads)" />
    </inputs>

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

    <outputs>
       <data format="tabular" name="report" label="Run/assembly summary" />
    </outputs>

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

    <tests>
        <test>
            <param name="in_raw1" value="sumrun_R1.fq" ftype="fastq" />
            <param name="in_raw2" value="sumrun_R2.fq" ftype="fastq" />
            <param name="in_filt1" value="sumrun_sync_R1.fq" ftype="fastq" />
            <param name="in_filt2" value="sumrun_sync_R2.fq" ftype="fastq" />
            <param name="in_ref" value="sumrun_ref.fa" ftype="fasta" />
            <param name="in_bg" value="sumrun_ref.bg" ftype="bedgraph" />
            <param name="in_fqc1" value="sumrun_R1.fastqc" ftype="txt" />
            <param name="in_fqc2" value="sumrun_R2.fastqc" ftype="txt" />
            <output name="report" file="sumrun.report.tsv" compare="diff" />
        </test>
    </tests>

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

    <help>

    `summarize_run` is a Galaxy-only utility from BASE2BIO that reports a
    number of summary statistics for a sequencing run and assembly. It was
    written to support workflows at the USDA Southeast Poultry Research
    Laboratory and may be of limited general-purpose application.

    </help>

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

    <citations>
    </citations>

</tool>