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1 <tool id="annotateBed" name="Annotates">
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2
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3 <description> the depth & breadth of coverage of features from multiple files</description>
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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 <requirement type="package">bedtools</requirement>
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8 </requirements>
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2
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10 <command>
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11 annotateBed
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12 $countflag
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13 -i '$inputRegion'
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14 -names
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15 #for $i, $s in enumerate($annotateColumn)
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16 '${s.colname}'
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17 #end for
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18 -files
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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 format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" />
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28 <param name="countflag" type="select" label="What to report in the output: ">
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29 <option value="-counts" selected="true">the count of features in each file that overlap the regions</option>
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30 <option value="">fraction of the region covered by each feature</option>
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31 <option value="-both">Report the counts followed by the % coverage</option>
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32 </param>
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33 <repeat name="annotateColumn" title="Column">
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34 <param name="colname" type="text" label="Feature name" />
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35 <param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" />
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36 </repeat>
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37
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38 </inputs>
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39 <outputs>
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40 <data format="bed" name="output" label="${inputRegion.name} annotated" />
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41 </outputs>
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42
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43 <help>
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44
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45 **What it does**
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46
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47 This tool is used to annotate the regions in a bed file with features provided in multiple BED files.
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48
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49 ..class:: warningmark
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50
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51 This tool requires that bedtools__ has been installed on your system.
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52
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53 -----
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54
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55 </help>
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56
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57 </tool> |
