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1 <tool id="AP" name="annotatePeak" version="1.16.2">
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2 <requirements>
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3 <requirement type="package" version="3.2.1">R</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoPeakTable"</command>
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9 <inputs>
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10 <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
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11 <validator type="empty_field" message="This field is required."/>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="csv" name="annoPeakTable" label="peakAnno.csv"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="test">
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20 <element name="test-data">
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21 <collection type="data">
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22 <element name="DMR" value="test-data/DMR.bed"/>
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23 </collection>
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24 </element>
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25 </param>
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26 <output format="csv" name="annoPeakTable" label="test-data/annoPeakTable.csv"/>
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27 </test>
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28 </tests>
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29 <help>
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30 **Description**
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31 </help>
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32 <citations>
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33 DMR
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34 </citations>
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35 </tool>
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