Mercurial > repos > iuc > bedtools

annotate mergeBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 071c1c5d4bad
children
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rev   line source
64
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1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>combine overlapping/nearby intervals into a single 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 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 #if $input.ext == "bam"
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17 -bed
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18 #end if
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19 > '${output}'
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20 ]]></command>
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21 <inputs>
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22 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Merge the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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23 <param name="strand" type="select" label="Calculation based on strandedness?">
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24 <option value="" selected="true">Overlaps on either strand</option>
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25 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
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26 <option value="-S +">Force merge for forward strand only (-S +)</option>
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27 <option value="-S -">Force merge for reverse strand only (-S -)</option>
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28 </param>
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29 <param name="distance" argument="-d" type="integer" value="0"
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30 label="Maximum distance between features allowed for features to be merged"
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31 help="Default 0: overlapping and/or book-ended features are merged. Note: negative values enforce the number of b.p. required for overlap."/>
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32 <expand macro="print_header" />
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33 <expand macro="c_and_o_argument">
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34 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
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35 </expand>
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36 </inputs>
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37 <outputs>
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38 <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input" value="mergedBed1.bed" ftype="bed" />
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43 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
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44 <assert_command>
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45 <not_has_text text="-s "/>
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46 <not_has_text text="-S "/>
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47 <has_text text="-d 0"/>
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48 <not_has_text text="-c "/>
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49 <not_has_text text="-o "/>
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50 </assert_command>
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51 </test>
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52 <test>
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53 <param name="input" value="mergedBed2.bed" ftype="bed" />
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54 <param name="strand" value="-s" />
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55 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
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56 <assert_command>
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57 <has_text text="-s "/>
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58 <not_has_text text="-S "/>
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59 <has_text text="-d 0"/>
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60 <not_has_text text="-c "/>
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61 <not_has_text text="-o "/>
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62 </assert_command>
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63 </test>
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64 <test>
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65 <param name="input" value="mergedBed3.bed" ftype="bed" />
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66 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
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67 <assert_command>
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68 <not_has_text text="-s "/>
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69 <not_has_text text="-S "/>
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70 <has_text text="-d 0"/>
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71 <not_has_text text="-c "/>
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72 <not_has_text text="-o "/>
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73 </assert_command>
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74 </test>
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75 <test>
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76 <param name="input" value="mergedBed4.bed" ftype="bed" />
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77 <param name="distance" value="1000" />
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78 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
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79 <assert_command>
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80 <not_has_text text="-s "/>
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81 <not_has_text text="-S "/>
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82 <has_text text="-d 1000"/>
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83 <not_has_text text="-c "/>
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84 <not_has_text text="-o "/>
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85 </assert_command>
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86 </test>
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87 <test>
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88 <param name="input" value="mergedBed4.bed" ftype="bed" />
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89 <param name="distance" value="1000" />
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90 <repeat name="c_and_o_argument_repeat">
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91 <param name="col" value="1"/>
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92 <param name="operation" value="count"/>
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93 </repeat>
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94 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
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95 <assert_command>
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96 <not_has_text text="-s "/>
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97 <not_has_text text="-S "/>
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98 <has_text text="-d 1000"/>
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99 <has_text text="-c 1"/>
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100 <has_text text="-o count"/>
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101 </assert_command>
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102 </test>
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103 </tests>
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104 <help><![CDATA[
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105 **What it does**
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106
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107 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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108
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109
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110 .. image:: $PATH_TO_IMAGES/merge-glyph.png
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111
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112
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113 .. class:: warningmark
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114
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115 bedtools merge requires that you presort your data by chromosome and then by start position.
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116
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117
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118 ==========================================================================
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119 Default behavior
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120 ==========================================================================
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121 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
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122 bookended intervals into a single, "flattened" or "merged" interval.
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123
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iuc
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124 ::
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iuc
parents:
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125
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iuc
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126 $ cat A.bed
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iuc
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127 chr1 100 200
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iuc
parents:
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128 chr1 180 250
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iuc
parents:
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129 chr1 250 500
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iuc
parents:
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130 chr1 501 1000
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iuc
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131
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iuc
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132 $ bedtools merge -i A.bed
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iuc
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133 chr1 100 500
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iuc
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134 chr1 501 1000
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iuc
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135
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iuc
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136
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iuc
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137 ==========================================================================
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iuc
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138 *-s* Enforcing "strandedness"
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iuc
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139 ==========================================================================
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iuc
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140 The ``-s`` option will only merge intervals that are overlapping/bookended
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iuc
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141 *and* are on the same strand.
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142
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iuc
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143 ::
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iuc
parents:
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144
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iuc
parents:
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145 $ cat A.bed
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iuc
parents:
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146 chr1 100 200 a1 1 +
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iuc
parents:
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147 chr1 180 250 a2 2 +
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iuc
parents:
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148 chr1 250 500 a3 3 -
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iuc
parents:
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149 chr1 501 1000 a4 4 +
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iuc
parents:
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150
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iuc
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151 $ bedtools merge -i A.bed -s
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iuc
parents:
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152 chr1 100 250 +
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iuc
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153 chr1 501 1000 +
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iuc
parents:
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154 chr1 250 500 -
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iuc
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155
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iuc
parents:
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156
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157 ==========================================================================
26
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158 *-d* Controlling how close two features must be in order to merge
8
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159 ==========================================================================
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160 By default, only overlapping or book-ended features are combined into a new
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161 feature. However, one can force ``merge`` to combine more distant features
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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162 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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163 features that overlap or are within 1000 base pairs of one another will be
8
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iuc
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164 combined.
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165
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parents:
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166 ::
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iuc
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167
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iuc
parents:
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168 $ cat A.bed
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iuc
parents:
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169 chr1 100 200
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iuc
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170 chr1 501 1000
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171
8
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iuc
parents:
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172 $ bedtools merge -i A.bed
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iuc
parents:
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173 chr1 100 200
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iuc
parents:
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174 chr1 501 1000
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iuc
parents:
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175
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iuc
parents:
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176 $ bedtools merge -i A.bed -d 1000
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iuc
parents:
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177 chr1 100 200 1000
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iuc
parents:
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178
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iuc
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179
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iuc
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180 @REFERENCES@
50
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iuc
parents: 48
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181 ]]></help>
8
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iuc
parents:
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182 <expand macro="citations" />
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iuc
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183 </tool>