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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 <![CDATA[
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10 bedtools window
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11 #if $inputA.ext == "bam":
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12 -abam $inputA
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13 #else:
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14 -a $inputA
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15 #end if
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16 -b $inputB
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17 $bed
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18 $strandB
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19 #if $addition.addition_select == 'window':
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20 -w $addition.w
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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 ]]>
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31 </command>
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32 <inputs>
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33 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
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34 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
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35 <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
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36 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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37 help="(-bed)" />
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38 <conditional name="addition">
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39 <param name="addition_select" type="select" label="Choose what you want to do">
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40 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
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41 <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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42 </param>
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43 <when value="window">
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44 <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
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45 </when>
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46 <when value="lr">
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47 <param name="l" type="integer" value="1000"
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48 label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
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49 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" />
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50 <param name="r" type="integer" value="1000"
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51 label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
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52 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" />
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53 </when>
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54 </conditional>
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55 <param name="strandB" type="select" label="Calculation based on strandedness?">
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56 <option value="" selected="True">Report any hit in B</option>
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57 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
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58 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
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59 </param>
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60 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue=""
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61 label="Write original A entry once if any overlaps found in B"
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62 help="In other words, just report the fact at least one overlap was found in B. (-u)" />
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63 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue=""
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64 label="For each entry in A, report the number of hits in B"
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65 help="Reports 0 for A entries that have no overlap with B (-c)" />
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66 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue=""
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67 label="Only report those entries in A that have no overlaps with B" help="(-v)" />
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68 <expand macro="print_header" />
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69 </inputs>
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70 <outputs>
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71 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
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72 </outputs>
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1
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73 <tests>
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74 <test>
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75 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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76 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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77 <output name="output" file="windowBed_result1.bed" ftype="bed" />
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78 </test>
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79 <test>
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80 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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81 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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82 <param name="addition_select" value="window" />
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83 <param name="w" value="5000" />
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84 <output name="output" file="windowBed_result2.bed" ftype="bed" />
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85 </test>
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86 <test>
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87 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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88 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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89 <param name="addition_select" value="lr" />
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90 <param name="l" value="200" />
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91 <param name="r" value="20000" />
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92 <output name="output" file="windowBed_result2.bed" ftype="bed" />
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93 </test>
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94 </tests>
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95 <help>
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96 <![CDATA[
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97 **What it does**
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98
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99 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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100
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101 .. image:: $PATH_TO_IMAGES/window-glyph.png
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102
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103 @REFERENCES@
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104 ]]>
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105 </help>
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106 <expand macro="citations" />
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107 </tool>
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