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1 <?xml version="1.0"?>
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2 <tool_dependency>
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101
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3 <package name="R_3_0_1" version="3.0.1">
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4 <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="perl" version="5.18.1">
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7 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <set_environment version="1.0">
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10 <environment_variable action="set_to" name="MICLIP_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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11 </set_environment>
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12 <package name="miclip" version="1.2">
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13 <install version="1.0">
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14 <actions>
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15 <action type="setup_r_environment">
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16 <repository changeset_revision="4666f68ad4d5" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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17 <package name="R_3_0_1" version="3.0.1" />
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18 </repository>
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19 <package>https://github.com/bgruening/download_store/raw/master/miclip/moments_0.13.tar.gz</package>
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20 <package>https://github.com/bgruening/download_store/raw/master/miclip/VGAM_0.9-3.tar.gz</package>
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21 <package>https://github.com/bgruening/download_store/raw/master/miclip/MiClip_1.2.tar.gz</package>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>
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26 MiClip: A Model-based Approach to Identify Binding Sites in CLIP-Seq Data
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27 Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data.
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28 http://cran.r-project.org/web/packages/MiClip/
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29 </readme>
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30 </package>
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31 </tool_dependency>
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