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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" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore" "$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 <param name="annoData" type="select" label="annoData" help="choose your annoData human or mice">
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14 <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option>
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15 <option name="mice" type="text" value="EnsDb.Mmusculus.v75">Mice</option>
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16 </param>
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17 <param name="bindingType" type="select" label="bindingType" help="choose bindingType">
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18 <option name="sS" type="text" value="startSite">startSite</option>
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19 <option name="eS" type="text" value="endSite">endSite</option>
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20 <option name="fR" type="text" value="fullRange">fullRange</option>
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21 </param>
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22 <param name="ignore" type="select" label="ignore.peak.strand" help="choose TRUE or FALSE">
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23 <option name="T" type="text" value="TRUE">true</option>
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24 <option name="F" type="text" value="FALSE">false</option>
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25 </param>
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26 <param name="upstream" type="text" value=""
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27 label="upstream - number no bigger than 0"
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28 help="e.g. '-5000'" >
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29 </param>
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30 <param name="downstream" type="text" value=""
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31 label="downstream - number no less than 1"
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32 help="e.g. '5000'" >
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data format="txt" name="annoPeakTable" label="peakAnno.txt"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="test">
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41 <element name="test-data">
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42 <collection type="data">
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43 <element name="DMR" value="test-data/DMR.bed"/>
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44 </collection>
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45 </element>
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46 </param>
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47 <output format="txt" name="annoPeakTable" label="test-data/annoPeakTable.txt"/>
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48 </test>
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49 </tests>
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50 <help>
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51 **Description**
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52 </help>
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53 <citations>
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54 DMR
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55 </citations>
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56 </tool>
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