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<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie" version="0.12.7">
        <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="vienna_rna" version="1.8.5">
        <repository changeset_revision="263ded3da06c" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pdf_api2" version="2.023">
        <repository changeset_revision="356e5d565b9f" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="mirdeep2_quantifier" version="2.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action>
                <action type="move_file">
                    <source>quantifier.pl</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>make_html2.pl</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>convert_bowtie_output.pl</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 
First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. 
By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. 
The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.

        </readme>
    </package>
</tool_dependency>