<tool id="ivar_getmasked" name="ivar getmasked" version="@VERSION@+galaxy0">
    <description>Detect primer mismatches and get primer indices for the amplicon to be masked</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        ivar getmasked 
        -i '$filtered_tsv' 
        -b '$primers_bed'
        -f '$primers_tsv'
        -p masked_primers
    ]]>    </command>
    <inputs>
        <param name="filtered_tsv" argument="-i" type="data" format="tabular,txt" label="Input filtered variants tsv generated from filtervariants"/>
        <param name="primers_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
        <param name="primers_tsv" argument="-f" type="data" format="tabular" label="Primer pair information file containing left and right primer names for the same amplicon"/>
    </inputs>
    <outputs>
        <data name="masked" format="txt" label="${tool.name} on ${on_string} Output" from_work_dir="masked_primers.txt"/>
    </outputs>
    <tests>
        <test>
            <param name="filtered_tsv" value="zika/primers_Z52_consensus.tsv"/>
            <param name="primers_bed" value="zika/db/zika_primers_consensus.bed"/>
            <param name="primers_tsv" value="zika/db/pair_information.tsv"/>
            <output name="masked" file="zika/primer_mismatchers_indices.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        iVar uses a .tsv file with variants to get the zero based indices (based on
        the BED file) of mismatched primers. This command requires another .tsv file
        with each line containing the left and right primer names separated by a
        tab. This is used to get both the primers for an amplicon with a single
        mismatched primer. The output is a text file with the zero based primer
        indices delimited by a space. The output is written to a a text file using
        the prefix provided.
        
        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
    ]]>    </help>
    <expand macro="citations" />
</tool>