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1 <tool id="bedtools_tagbed" name="TagBed" 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 tag
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10 -i $inputA
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11 -files
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12 #for $bed in beds:
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13 $bed.input
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14 #end for
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15 -f $overlap
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16 $strand
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17 -tag $tag
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18 $field
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19 > $output
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20 </command>
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21 <inputs>
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22 <param format="bam" name="inputA" type="data" label="BAM file"/>
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23
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24 <repeat name="beds" title="Add files" >
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25 <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" />
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26 </repeat>
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27 <expand macro="strand2" />
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28 <expand macro="overlap" />
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29
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30 <param name="tag" type="text" value="YB" label="Dictate what the tag should be." />
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31 <param name="field" type="select" label="Use which field from the annotation files to populate tags?">
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32 <option value="-labels" selected="True">labels</option>
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33 <option value="-scores">Scores</option>
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34 <option value="-names">Names</option>
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35 <option value="-labels -intervals">Intervals</option>
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36 </param>
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37 </inputs>
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38 </inputs>
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39
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40 <outputs>
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41 <data format="bed" name="output" label="" />
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42 </outputs>
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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 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
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48
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49 @REFERENCES@
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50
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51 </help>
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52 </tool>
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