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1 <tool id="bedtools_windowbed" name="WindowBed" 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 window
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10 #if $inputA.ext == "bam":
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11 -abam $inputA
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12 #else:
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13 -a $inputA
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14 #end if
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15 -b $inputB
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16 $ubam
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17 $bed
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18 $strandB
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19 #if $addition.addition_select == 'b':
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20 -w $addition.b
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21 #elif $addition.addition_select == 'lr':
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22 -l $addition.l
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23 -r $addition.r
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24 #end if
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25 $original
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26 $number
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27 $nooverlaps
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28 $header
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29 > $output
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30 </command>
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31 <inputs>
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32 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
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33 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
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34 <param name="ubam" type="boolean" checked="false" truevalue="-ubam" falsevalue="" label="Write uncompressed BAM output" />
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35 <param name="bed" type="boolean" checked="false" truevalue="bed" falsevalue="" label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file" />
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36 <conditional name="addition">
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37 <param name="addition_select" type="select" label="Choose what you want to do">
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38 <option value="huhn" selected="True">Do not change added base pairs</option>
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39 <option value="b">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
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40 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
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41 </param>
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42 <when value="b">
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43 <param name="b" label="Give Value" type="integer" value="1000" />
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44 </when>
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45 <when value="lr">
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46 <param name="l" label="Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000" />
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47 <param name="r" label="Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. Allows one to create assymetrical “windows”. Default is 1000bp" type="integer" value="1000" />
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48 </when>
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49 </conditional>
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50 <param name="strandB" type="select" label="Calculation based on strandedness?">
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51 <option value="" selected="True">Report any hit in B</option>
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52 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
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53 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
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54 </param>
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55 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue="" label="Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B" />
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56 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" label="For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B" />
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57 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Only report those entries in A that have no overlaps with B" />
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58 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the A file prior to results" />
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59
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60 </inputs>
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61 <outputs>
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62 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
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63 </outputs>
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64 <help>
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65
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66 **What it does**
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67
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68 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
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69
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70 .. image:: $PATH_TO_IMAGES/window-glyph.png
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71
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72 @REFERENCES@
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73 </help>
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74 <expand macro="citations" />
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75 </tool>
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