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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 <![CDATA[
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10 bedtools slop
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11 $pct
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12 $strand
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13 -g $genome
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14 -i $inputA
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15 #if $addition.addition_select == 'b':
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16 -b $addition.b
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17 #else:
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18 -l $addition.l
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19 -r $addition.r
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20 #end if
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21 $header
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22 > $output
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
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27 <expand macro="genome" />
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28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
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29 label="Define -l and -r as a fraction of the feature’s length"
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30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
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31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
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32 label="Define -l and -r based on strand"
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33 help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
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34 <expand macro="addition" />
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35 <expand macro="print_header" />
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36 </inputs>
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37 <outputs>
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38 <data format="bed" name="output"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="inputA" value="a.bed" ftype="bed" />
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43 <param name="genome" value="mm9_chr1.len" ftype="bed" />
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44 <param name="addition_select" value="b" />
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45 <param name="b" value="5" />
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46 <output name="output" file="slopBed_result1.bed" ftype="bed" />
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47 </test>
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48 <test>
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49 <param name="inputA" value="a.bed" ftype="bed" />
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50 <param name="genome" value="mm9_chr1.len" ftype="bed" />
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51 <param name="addition_select" value="lr" />
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52 <param name="l" value="2" />
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53 <param name="r" value="3" />
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54 <output name="output" file="slopBed_result2.bed" ftype="bed" />
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55 </test>
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56 </tests>
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57 <help>
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58 <![CDATA[
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59 **What it does**
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60
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61 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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62
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63 .. image:: $PATH_TO_IMAGES/slop-glyph.png
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64
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65 .. class:: warningmark
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66
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67 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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68 @REFERENCES@
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69 ]]>
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70 </help>
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71 <expand macro="citations" />
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72 </tool>
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