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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
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4 </description>
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5
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6 <requirements>
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7 <requirement type="binary">annotateBed</requirement>
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8 <requirement type="package">bedtools</requirement>
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9 </requirements>
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10
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11 <command>
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12 annotateBed
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13 $countflag
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14 -i '$inputRegion'
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15 -names
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16 #for $i, $s in enumerate($annotateColumn)
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17 '${s.colname}'
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18 #end for
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19 -files
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20 #for $i, $s in enumerate($annotateColumn)
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21 '${s.colfile}'
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22 #end for
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23 > '$output'
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24 </command>
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25
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26 <inputs>
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27
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28 <param format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" />
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29 <param name="countflag" type="select" label="What to report in the output: ">
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30 <option value="-counts" selected="true">the count of features in each file that overlap the regions</option>
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31 <option value="">fraction of the region covered by each feature</option>
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32 <option value="-both">Report the counts followed by the % coverage</option>
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33 </param>
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34 <repeat name="annotateColumn" title="Column">
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35 <param name="colname" type="text" label="Feature name" />
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36 <param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" />
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37 </repeat>
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38
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39 </inputs>
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40 <outputs>
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41 <data format="bed" name="output" label="${inputRegion.name} annotated" />
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42 </outputs>
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43
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44 <help>
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45
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46 **What it does**
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47
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48 This tool is used to annotate the regions in a bed file with features provided in multiple BED files.
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49
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50 .. class:: warningmark
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51
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52 This tool requires that bedtools__ has been installed on your system.
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53
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54 -----
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55
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56 .. __: http://code.google.com/p/bedtools/
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57
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58 </help>
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59
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60 </tool> |
