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1 <tool id="bedtools_flankbed" name="FlankBed" 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 flankBed
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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 $input
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15
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16 #if $addition.addition_select == 'b':
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17 -b $addition.b
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18 #else:
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19 -l $addition.l
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20 -r $addition.r
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21 #end if
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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="input" 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="For example. 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 </inputs>
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36 <outputs>
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37 <data metadata_source="input" format_source="input" name="output" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="a.bed" ftype="bed" />
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42 <param name="genome" value="mm9_chr1.len"/>
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43 <param name="addition_select" value="b"/>
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44 <param name="b" value="5"/>
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45 <output name="output" file="flankBed_result1.bed" ftype="bed" />
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46 </test>
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47 <test>
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48 <param name="input" value="a.bed" ftype="bed" />
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49 <param name="genome" value="mm9_chr1.len"/>
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50 <param name="addition_select" value="lr"/>
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51 <param name="l" value="2"/>
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52 <param name="r" value="3"/>
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53 <output name="output" file="flankBed_result2.bed" ftype="bed" />
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58 **What it does**
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59
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60 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
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61
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62 .. image:: $PATH_TO_IMAGES/flank-glyph.png
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63
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64 .. class:: warningmark
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65
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66 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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67
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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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