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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="perl" version="5.18.1">
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4 <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bowtie" version="0.12.7">
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7 <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="vienna_rna" version="1.8.5">
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10 <repository changeset_revision="263ded3da06c" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="pdf_api2" version="2.023">
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13 <repository changeset_revision="356e5d565b9f" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="mirdeep2_quantifier" version="2.0">
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16 <install version="1.0">
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17 <actions>
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18 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action>
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19 <action type="move_file">
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20 <source>quantifier.pl</source>
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21 <destination>$INSTALL_DIR</destination>
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22 </action>
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23 <action type="move_file">
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24 <source>make_html2.pl</source>
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25 <destination>$INSTALL_DIR</destination>
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26 </action>
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27 <action type="move_file">
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28 <source>convert_bowtie_output.pl</source>
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29 <destination>$INSTALL_DIR</destination>
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30 </action>
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31 <action type="set_environment">
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32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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33 </action>
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34 </actions>
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35 </install>
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36 <readme>
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37
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38 The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs.
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39 First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too.
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40 By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors.
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41 The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
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42
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43 </readme>
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44 </package>
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45 </tool_dependency>
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