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1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
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2 <description>(mergeBed)</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 mergeBed
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10 -i $input
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11 $strandedness
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12 $report_number
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13 -d $distance
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14 $nms
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15 #if str($scores) != 'none'
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16 -scores $scores
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17 #end if
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18 > $output
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19 </command>
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20 <inputs>
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21 <param name="input" format="bed,gff,vcf" type="data" label="Sort the following BED/VCF/GFF file"/>
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22 <param name="strandedness" type="boolean" label="Force strandedness." truevalue="-s" falsevalue="" checked="false"
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23 help="That is, only merge features that are the same strand."/>
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24 <param name="report_number" type="boolean" label="Report the number of BED entries that were merged." truevalue="-n" falsevalue="" checked="false"
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25 help="1 is reported if no merging occurred."/>
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26 <param name="nms" type="boolean" label="Report the names of the merged features separated by commas." truevalue="-nms" falsevalue="" checked="false"
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27 help="1 is reported if no merging occurred."/>
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28
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29 <param name="distance" type="integer" value="0" label="Maximum distance between features allowed for features to be merged."
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30 help="That is, overlapping and/or book-ended features are merged."/>
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31 <param name="scores" type="select" label="Report the scores of the merged features as">
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32 <option value="none" selected="True">Do not report at all</option>
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33 <option value="sum">Sum</option>
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34 <expand macro="math_options" />
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="bed" name="output" 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="0.bed" ftype="bed" />
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43 <output name="output" file="0_result.bed" ftype="bed" />
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44 </test>
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45 <test>
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46 <param name="input" value="1.bed" ftype="bed" />
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47 <param name="strandedness" value="-s" />
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48 <output name="output" file="1_result.bed" ftype="bed" />
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49 </test>
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50 <test>
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51 <param name="input" value="2.bed" ftype="bed" />
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52 <param name="report_number" value="-n" />
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53 <output name="output" file="2_result.bed" ftype="bed" />
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54 </test>
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55 <test>
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56 <param name="input" value="3.bed" ftype="bed" />
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57 <param name="distance" value="1000" />
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58 <output name="output" file="3_result.bed" ftype="bed" />
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59 </test>
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60 </tests>
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61 <help>
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62
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63 **What it does**
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64
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65 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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66
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67
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68 .. image:: $PATH_TO_IMAGES/merge-glyph.png
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69
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70
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71 .. class:: warningmark
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72
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73 bedtools merge requires that you presort your data by chromosome and then by start position.
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74
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75
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76 ==========================================================================
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77 Default behavior
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78 ==========================================================================
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79 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
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80 bookended intervals into a single, "flattened" or "merged" interval.
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81
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82 ::
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83
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84 $ cat A.bed
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85 chr1 100 200
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86 chr1 180 250
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87 chr1 250 500
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88 chr1 501 1000
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89
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90 $ bedtools merge -i A.bed
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91 chr1 100 500
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92 chr1 501 1000
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93
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94
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95 ==========================================================================
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96 *-s* Enforcing "strandedness"
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97 ==========================================================================
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98 The ``-s`` option will only merge intervals that are overlapping/bookended
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99 *and* are on the same strand.
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100
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101 ::
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102
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103 $ cat A.bed
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104 chr1 100 200 a1 1 +
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105 chr1 180 250 a2 2 +
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106 chr1 250 500 a3 3 -
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107 chr1 501 1000 a4 4 +
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108
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109 $ bedtools merge -i A.bed -s
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110 chr1 100 250 +
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111 chr1 501 1000 +
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112 chr1 250 500 -
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113
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114
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115 ==========================================================================
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116 *-n* Reporting the number of features that were merged
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117 ==========================================================================
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118 The -n option will report the number of features that were combined from the
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119 original file in order to make the newly merged feature. If a feature in the
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120 original file was not merged with any other features, a "1" is reported.
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121
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122 ::
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123
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124 $ cat A.bed
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125 chr1 100 200
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126 chr1 180 250
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127 chr1 250 500
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128 chr1 501 1000
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129
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130 $ bedtools merge -i A.bed -n
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131 chr1 100 500 3
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132 chr1 501 1000 1
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133
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134
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135 ==========================================================================
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136 *-d* Controlling how close two features must be in order to merge
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137 ==========================================================================
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138 By default, only overlapping or book-ended features are combined into a new
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139 feature. However, one can force ``merge`` to combine more distant features
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140 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
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141 features that overlap or are within 1000 base pairs of one another will be
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142 combined.
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143
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144 ::
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145
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146 $ cat A.bed
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147 chr1 100 200
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148 chr1 501 1000
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149
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150 $ bedtools merge -i A.bed
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151 chr1 100 200
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152 chr1 501 1000
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153
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154 $ bedtools merge -i A.bed -d 1000
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155 chr1 100 200 1000
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156
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157
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158 =============================================================
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159 *-nms* Reporting the names of the features that were merged
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160 =============================================================
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161 Occasionally, one might like to know that names of the features that were
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162 merged into a new feature. The ``-nms`` option will add an extra column to the
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163 ``merge`` output which lists (separated by semicolons) the names of the
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164 merged features.
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165
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166 ::
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167
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168 $ cat A.bed
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169 chr1 100 200 A1
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170 chr1 150 300 A2
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171 chr1 250 500 A3
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172
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173 $ bedtools merge -i A.bed -nms
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174 chr1 100 500 A1,A2,A3
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175
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176
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177 ===============================================================
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178 *-scores* Reporting the scores of the features that were merged
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179 ===============================================================
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180 Similarly, we might like to know that scores of the features that were
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181 merged into a new feature. Enter the ``-scores`` option. One can specify
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182 how the scores from each overlapping interval should be reported.
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183
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184 ::
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185
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186 $ cat A.bed
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187 chr1 100 200 A1 1
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188 chr1 150 300 A2 2
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189 chr1 250 500 A3 3
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190
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191 $ bedtools merge -i A.bed -scores mean
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192 chr1 100 500 2
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193
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194 $ bedtools merge -i A.bed -scores max
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195 chr1 100 500 3
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196
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197 $ bedtools merge -i A.bed -scores collapse
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198 chr1 100 500 1,2,3
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199
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200
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201 @REFERENCES@
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202 </help>
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203 <expand macro="citations" />
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204 </tool>
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