Mercurial > repos > iuc > bedtools

annotate mergeBed.xml @ 57:1d0a0d6a78b1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:02:26 +0000
parents 7a06bb42dbb1
children 539958feb49c
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1d0a0d6a78b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>combine overlapping/nearby intervals into a single interval</description>
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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 mergeBed
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11 -i '${input}'
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12 $strand
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13 -d $distance
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14 $header
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15 @C_AND_O_ARGUMENT@
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16 > '${output}'
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17 ]]></command>
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18 <inputs>
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19 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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20 <param name="strand" type="select" label="Calculation based on strandedness?">
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21 <option value="" selected="true">Overlaps on either strand</option>
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22 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
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23 <option value="-S +">Force merge for forward strand only (-S +)</option>
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24 <option value="-S -">Force merge for reverse strand only (-S -)</option>
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25 </param>
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26 <param name="distance" argument="-d" type="integer" value="0"
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27 label="Maximum distance between features allowed for features to be merged"
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28 help="That is, overlapping and/or book-ended features are merged"/>
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29 <expand macro="print_header" />
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30 <expand macro="c_and_o_argument">
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31 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
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32 </expand>
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="mergedBed1.bed" ftype="bed" />
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40 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
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41 </test>
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42 <test>
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43 <param name="input" value="mergedBed2.bed" ftype="bed" />
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44 <param name="strandedness" value="-s" />
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45 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
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46 </test>
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47 <test>
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48 <param name="input" value="mergedBed3.bed" ftype="bed" />
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49 <param name="report_number" value="-n" />
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50 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
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51 </test>
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52 <test>
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53 <param name="input" value="mergedBed4.bed" ftype="bed" />
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54 <param name="distance" value="1000" />
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55 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
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56 </test>
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57 <test>
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58 <param name="input" value="mergedBed4.bed" ftype="bed" />
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59 <param name="distance" value="1000" />
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60 <repeat name="c_and_o_argument_repeat">
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61 <param name="col" value="1"/>
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62 <param name="operation" value="count"/>
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63 </repeat>
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64 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 **What it does**
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69
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70 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
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73 .. image:: $PATH_TO_IMAGES/merge-glyph.png
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76 .. class:: warningmark
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78 bedtools merge requires that you presort your data by chromosome and then by start position.
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79
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81 ==========================================================================
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82 Default behavior
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83 ==========================================================================
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84 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
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85 bookended intervals into a single, "flattened" or "merged" interval.
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86
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87 ::
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88
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89 $ cat A.bed
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90 chr1 100 200
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91 chr1 180 250
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92 chr1 250 500
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93 chr1 501 1000
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94
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95 $ bedtools merge -i A.bed
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96 chr1 100 500
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97 chr1 501 1000
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98
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100 ==========================================================================
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101 *-s* Enforcing "strandedness"
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102 ==========================================================================
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103 The ``-s`` option will only merge intervals that are overlapping/bookended
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104 *and* are on the same strand.
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105
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106 ::
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107
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108 $ cat A.bed
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109 chr1 100 200 a1 1 +
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110 chr1 180 250 a2 2 +
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111 chr1 250 500 a3 3 -
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112 chr1 501 1000 a4 4 +
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113
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114 $ bedtools merge -i A.bed -s
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115 chr1 100 250 +
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116 chr1 501 1000 +
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117 chr1 250 500 -
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118
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119
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120 ==========================================================================
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121 *-d* Controlling how close two features must be in order to merge
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122 ==========================================================================
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123 By default, only overlapping or book-ended features are combined into a new
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124 feature. However, one can force ``merge`` to combine more distant features
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125 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
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126 features that overlap or are within 1000 base pairs of one another will be
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127 combined.
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128
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129 ::
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130
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131 $ cat A.bed
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132 chr1 100 200
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133 chr1 501 1000
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134
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135 $ bedtools merge -i A.bed
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136 chr1 100 200
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137 chr1 501 1000
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138
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139 $ bedtools merge -i A.bed -d 1000
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140 chr1 100 200 1000
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141
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142
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143 @REFERENCES@
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144 ]]></help>
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145 <expand macro="citations" />
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146 </tool>