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