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1 <tool id="annotateBed" name="annotateBed">
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2
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3
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3 <description>Annotate BED files with overlapping BED files</description>
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7
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4
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5 <requirements>
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6 <requirement type="binary">annotateBed</requirement>
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8
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7 <requirement type="package">bedtools</requirement>
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7
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8 </requirements>
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9
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2
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10 <command>
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6
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11 annotateBed
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2
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12 $countflag
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13 -i '$inputRegion'
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14 -names
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5
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15 #for $i, $s in enumerate($annotateColumn)
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8
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16 '${s.colname}'
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17 #end for
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2
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18 -files
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5
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19 #for $i, $s in enumerate($annotateColumn)
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20 '${s.colfile}'
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21 #end for
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22 > '$output'
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23 </command>
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24
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25 <inputs>
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26
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27 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
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28 <param format="bed" name="inputRegion" type="data" label="The region to be annotated" />
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29 <repeat name="annotateColumn" title="Column">
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30 <param name="colname" type="text" label="Column name" />
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31 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
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32 </repeat>
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33
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34 </inputs>
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35 <outputs>
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36 <data format="bed" name="output" metadata_source="inputRegion" label="${inputRegion.name} annotated" />
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37 </outputs>
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38
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39 <help>
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40
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41 .. class:: infomark
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42
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43 IMPORTANT INFORMATION
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44
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45 ----
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46
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47 WRITE HELP HERE
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48
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49 </help>
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50
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51 </tool> |
