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annotate windowBed.xml @ 46:64e2edfe7a2c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
author iuc
date Sat, 18 May 2024 23:28:38 +0000
parents 7ab85ac5f64b
children
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>find overlapping intervals within a window around an interval</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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools window
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11 #if $inputA.is_of_type('bam'):
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12 -abam '$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 ]]></command>
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31 <inputs>
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32 <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
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33 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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34 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
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35 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="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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39 <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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40 </param>
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41 <when value="window">
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42 <param argument="-w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
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43 </when>
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44 <when value="lr">
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45 <param argument="-l" type="integer" value="1000"
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46 label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B"
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47 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
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48 <param argument="-r" type="integer" value="1000"
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49 label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B"
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50 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
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51 </when>
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52 </conditional>
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53 <param name="strandB" type="select" label="Calculation based on strandedness?">
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54 <option value="" selected="true">Report any hit in B</option>
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55 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
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56 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
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57 </param>
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58 <param name="original" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
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59 label="Write original A entry once if any overlaps found in B"
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60 help="In other words, just report the fact at least one overlap was found in B" />
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61 <param name="number" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
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62 label="For each entry in A, report the number of hits in B"
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63 help="Reports 0 for A entries that have no overlap with B" />
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64 <param name="nooverlaps" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
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65 label="Only report those entries in A that have no overlaps with B" />
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66 <expand macro="print_header" />
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67 </inputs>
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68 <outputs>
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69 <data name="output" format_source="inputA" metadata_source="inputA" />
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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74 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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75 <output name="output" file="windowBed_result1.bed" ftype="bed" />
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76 </test>
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77 <test>
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78 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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79 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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80 <param name="addition_select" value="window" />
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81 <param name="w" value="5000" />
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82 <output name="output" file="windowBed_result2.bed" ftype="bed" />
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83 </test>
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84 <test>
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85 <param name="inputA" value="windowBedA.bed" ftype="bed" />
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86 <param name="inputB" value="windowBedB.bed" ftype="bed" />
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87 <param name="addition_select" value="lr" />
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88 <param name="l" value="200" />
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89 <param name="r" value="20000" />
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90 <output name="output" file="windowBed_result2.bed" ftype="bed" />
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 **What it does**
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95
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96 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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97
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98 .. image:: $PATH_TO_IMAGES/window-glyph.png
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99
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100 @REFERENCES@
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101 ]]></help>
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102 <expand macro="citations" />
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103 </tool>