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1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="0.2.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 bedtools annotate
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10 -i $inputA
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11 -files
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12 #for $bed in $names.beds:
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13 $bed.input
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14 #end for
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15
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16 #if names.names_select == 'yes':
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17 -names
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18 #for $bed in $names.beds:
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19 $bed.inputName
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20 #end for
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21 #end if
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22 $strand
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23 $counts
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24 $both
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25 > $output
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26 </command>
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27 <inputs>
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28 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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29 <!-- Additional files, if the user needs more -->
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30 <conditional name="names">
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31 <param name="names_select" type="select" label="Specify names for each file">
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32 <option value="no" selected="True">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <when value="yes">
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36 <repeat name="beds" title="Add BED files and names" >
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37 <param name="input" format="bed" type="data" label="BED file" />
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38 <param name="inputName" type="text" label="Name of the file" />
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39 </repeat>
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40 </when>
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41 <when value="no">
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42 <repeat name="beds" title="Add BED files" >
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43 <param name="input" format="bed" type="data" label="BED file" />
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44 </repeat>
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45 </when>
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46 </conditional>
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47
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48 <expand macro="strand2" />
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49 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." />
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50 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." />
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51 </inputs>
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52 </inputs>
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53
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54 <outputs>
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55 <data format="bed" name="output" label="" />
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56 </outputs>
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57 <help>
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58
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59 **What it does**
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60
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61 bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
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62
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63 @REFERENCES@
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64
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65 </help>
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66 </tool>
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