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1 <tool id="bedtools_slopbed" name="SlopBed" 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 bedtools slop
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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 #if $addition.addition_select == 'b':
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15 -b $addition.b
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16 #else:
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17 -l $addition.l
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18 -r $addition.r
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19 #end if
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20 $header
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21
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22 > $output
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23 </command>
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24 <inputs>
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25 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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26 <expand macro="genome" />
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27 <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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28 <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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29 <expand macro="addition" />
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30 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the input file prior to results." />
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31 </inputs>
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32 <outputs>
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33 <data format="bed" name="output" label=""/>
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34 </outputs>
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35 <help>
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36
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37 **What it does**
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38
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39 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).
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40
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41 .. image:: $PATH_TO_IMAGES/slop-glyph.png
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42
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43 .. class:: warningmark
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44
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45 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
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46 @REFERENCES@
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47 </help>
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48 <expand macro="citations" />
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49 </tool>
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