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