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<?xml version="1.0" encoding="UTF-8"?>
<tool id="elastic_bowtie2" name="elastic bowtie2" version="1.0.0">
    <macros>
        <import>elastic_tool_wrappers_macros.xml</import>
    </macros>
    <description/>
    <requirements>
        <expand macro="rmarkdown_requirements"/>
    </requirements>
    <expand macro="stdio"/>
    <expand macro="shell_command"/>
    <inputs>
        <expand macro="tool_name"/>
        <expand macro="option_argument_single_dataset"/>
        <expand macro="option_argument_multiple_datasets"/>
        <expand macro="option_argument_path_relative_to_a_tool"/>
        <expand macro="option_argument_path_relative_to_this_tool"/>
        <expand macro="option_argument_string_float_integer"/>
    </inputs>
    <outputs>
        <expand macro="output_set"/>
        <citation type="bibtex"><![CDATA[
            @article{langmead2012fast,
                title={Fast gapped-read alignment with Bowtie 2},
                author={Langmead, Ben and Salzberg, Steven L},
                journal={Nature methods},
                volume={9},
                number={4},
                pages={357},
                year={2012},
                publisher={Nature Publishing Group}
            }
        ]]></citation>
    </outputs>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>