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1 <tool id="bedtools_tagbed" name="TagBed" version="@WRAPPER_VERSION@.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 <![CDATA[
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10 #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
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11 bedtools tag
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12 -i "${inputA}"
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13 -files "${files}"
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14 -f $overlap
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15 $strand
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16 -tag "${tag}"
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17 $field
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18 > "${output}"
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="inputA" format="bam" type="data" label="BAM file"/>
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23 <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
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24 <expand macro="strand2" />
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25 <expand macro="overlap" />
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26 <param name="tag" type="text" value="YB" label="Specify the tag to use" />
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27 <param name="field" type="select" label="Field from the annotation files to populate tags?">
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28 <option value="-labels" selected="True">Labels</option>
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29 <option value="-scores">Scores</option>
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30 <option value="-names">Names</option>
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31 <option value="-labels -intervals">Intervals</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data format="bam" name="output"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="inputA" value="srma_in3.bam" ftype="bam" />
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40 <param name="inputB" value="tagBed1.bed" ftype="bed" />
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41 <param name="field" value="-names" />
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42 <output name="output" file="tagBed_result1.bam" ftype="bam" />
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43 </test>
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44 </tests>
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45 <help>
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46 <![CDATA[
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47 **What it does**
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48
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49 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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50
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51 @REFERENCES@
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52 ]]>
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53 </help>
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54 <expand macro="citations" />
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55 </tool>
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