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1 <tool id="bedtools_flankbed" name="FlankBed" 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 flankBed
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10 $pct
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11 $strand
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12 -g $genome
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13 -i $inputA
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14 > $output
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15 #if addition.addition_select = 'b':
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16 -b $b
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17 #else:
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18 -l $l
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19 -r $r
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20 #end if
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21 </command>
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22 <inputs>
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23 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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24 <expand macro="genome" />
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25 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
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26 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
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27 <expand macro="conditional" />
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28
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29
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30 </inputs>
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31 <outputs>
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32 <data format="bed" name="output" label=""/>
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33 </outputs>
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34 <help>
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35
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36 **What it does**
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37
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38 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
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39
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40 .. image:: $PATH_TO_IMAGES/flank-glyph.png
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41
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42 .. class:: warningmark
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43
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44 In order to prevent creating intervals that violate chromosome boundaries, bedtools flank requires a genome file defining the length of each chromosome or contig.
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45
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46 @REFERENCES@
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47 </help>
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48 </tool>
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