<tool id="filter_tradis_tags" name="filter tradis tags" version="@VERSION@">
    <description>Filters a BAM file and outputs reads with tag matching -t option.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    
    filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered

    ]]>    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
        <param name="tag" type="text" label="Tags to filter" help="" />
        <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" />
        <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" />
    </inputs>

    <outputs>
        <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" />
    </outputs>

    <!-- <tests>
    </tests> -->
    <help><![CDATA[
        Adds transposon sequence and quality tags to the read strings and
        outputs a BAM.

        Usage: add_tags -b file.bam [options]

        Options:
        -b  : bam file with tradis tags
        -v  : verbose debugging output
    ]]>    </help>
    <expand macro="citations" />

</tool>