<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy0">
    <description>Remove reads from trimmed BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_bam' sorted.bam &&
        ln -s '$primer_index' primers.txt &&
        ln -s '$input_bed' bed.bed &&
        ivar removereads 
        -i sorted.bam 
        -p removed_reads.bam
        -t primers.txt 
        -b bed.bed
    ]]>    </command>
    <inputs>
        <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
        <param name="primer_index" argument="-t" type="data" format="txt" label="Text file with primer indices separated by spaces" help="This is the output of getmasked command"/>
        <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
            <param name="primer_index" value="zika/primer_mismatchers_indices.txt"/>
            <param name="input_bed" value="zika/db/zika_primers.bed"/>
            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
        </test>
    </tests>
    <help><![CDATA[
        This command accepts an aligned and sorted BAM file trimmed using ivar trim
        and removes the reads corresponding to the supplied primer indices, which is
        the output of ivar getmasked command. Under the hood, ivar trim adds the
        zero based primer index (based on the BED file) to the BAM auxillary data for
        every read. Hence, ivar removereads will only work on BAM files that have
        been trimmed using ivar trim.
        
        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
    ]]>    </help>
    <expand macro="citations" />
</tool>