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