<tool id="b2b_bam2consensus" name="BAM to consensus" version="0.003">

    <description>Re-call consensus based on BAM mapping</description>

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

    <requirements>
    <!--
        <requirement type="package" version="0.003">b2b-utils</requirement>
    -->
        <requirement type="package" version="7.407">mafft</requirement>
        <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
        <requirement type="package" version="6.1">ncurses</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="0.006007">perl-biox-seq</requirement>
        <requirement type="package" version="1.23">perl-file-which</requirement>
    </requirements>

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

    <version_command>bam2consensus --version | perl -wnE'print "$1\n" for /bam2consensus v(.+)/g'</version_command>

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

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

    ln -s $ref_file ref.tmp;
    ln -s $in_bam in.bam;
    samtools faidx ref.tmp;
    samtools index in.bam;

    bam2consensus
        --ref ref.tmp
        --bam in.bam
        --min_qual $min_qual
        --min_depth $min_depth
        --trim $trim
        --window $window
        --bg_bin_figs $bg_bin_figs
        --verbose
        #if $output_fasta:
            --consensus $out_fasta
        #end if
        #if $output_tsv:
            --table $out_tsv
        #end if
        #if $output_bg:
            --bedgraph $out_bg
        #end if
    ]]>
    </command>

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

    <inputs>
        <param name="in_bam" type="data" format="bam" label="BAM mapping file to use for consensus calling" help="BAM format" />
        <param name="ref_file" type="data" format="fasta" label="Reference sequence used for generating BAM" help="FASTA format" />
        <param argument="min_qual" size="4" type="integer" value="10" min="0" label="Minimum base quality to use for frequency calculations" />
        <param argument="min_depth" size="4" type="integer" value="3" min="0" label="Minimum consensus depth to call a base (otherwise called as N)" />
        <param argument="trim" size="4" type="float" value="0.2" min="0" label="Fraction to trim from each end when calculating trimmed mean of error window" />
        <param argument="window" size="4" type="integer" value="30" min="3" label="Size of sliding window used to calculate local error rates" />
        <param argument="bg_bin_figs" size="4" type="integer" value="0" min="0" label="Number of sig figs used to bin bedgraph depths (0 = no binning)" />
	    <param name="output_fasta" type="boolean" label="Output FASTA consensus" />
	    <param name="output_tsv" type="boolean" label="Output consensus/frequency table (tab-delim)" />
	    <param name="output_bg" type="boolean" label="Output bedgraph coverage file" />
    </inputs>

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

    <outputs>
        <data name="out_fasta" format="fasta" label="consensus (FASTA)">
            <filter>output_fasta is True</filter>
        </data>
        <data name="out_tsv" format="tabular" label="frequency table (tab-delim)">
            <filter>output_tsv is True</filter>
        </data>
        <data name="out_bg" format="bedgraph" label="coverage depth (bedgraph)">
            <filter>output_bg is True</filter>
        </data>
    </outputs>

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

    <tests>
        <test>
            <param name="in_bam" value="b2c.bam" ftype="bam" />
            <param name="ref_file" value="b2c.mod.fa" ftype="fasta" />
            <param name="min_qual" value="8" />
            <param name="min_depth" value="3" />
            <param name="bg_bin_figs" value="1" />
            <param name="output_fasta" value="True" />
            <param name="output_tsv" value="True" />
            <param name="output_bg" value="True" />
            <output name="out_fasta" file="b2c.out.fa" compare="diff" />
            <output name="out_tsv" file="b2c.out.tsv" compare="diff" />
            <output name="out_bg" file="b2c.out.bg" compare="diff" />
        </test>
    </tests>

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    <help>

    bam2consensus is a utility from b2b-utils for calling a new consensus
    sequence (and producing associated coverage depth and tabular outputs)
    based on raw read mapping to a genome assembly.

    </help>

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

    <citations>
    </citations>

</tool>