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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 <![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 $header
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15 > "${output}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF 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.</option>
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23 <option value="-S +">Force merge for forward strand only.</option>
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24 <option value="-S -">Force merge for reverse strand only.</option>
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25 </param>
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26 <param name="distance" 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. (-d)"/>
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29 <expand macro="print_header" />
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30 <expand macro="choose_columns" />
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31 <expand macro="choose_operations">
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32 <expand macro="math_options" />
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33 <expand macro="additional_math_options" />
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34 </expand>
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35 </inputs>
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36 <outputs>
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37 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="mergedBed1.bed" ftype="bed" />
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42 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
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43 </test>
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44 <test>
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45 <param name="input" value="mergedBed2.bed" ftype="bed" />
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46 <param name="strandedness" value="-s" />
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47 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
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48 </test>
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49 <test>
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50 <param name="input" value="mergedBed3.bed" ftype="bed" />
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51 <param name="report_number" value="-n" />
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52 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
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53 </test>
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54 <test>
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55 <param name="input" value="mergedBed4.bed" ftype="bed" />
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56 <param name="distance" value="1000" />
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57 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 **What it does**
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63
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64 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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65
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66
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67 .. image:: $PATH_TO_IMAGES/merge-glyph.png
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68
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69
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70 .. class:: warningmark
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71
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72 bedtools merge requires that you presort your data by chromosome and then by start position.
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73
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74
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75 ==========================================================================
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76 Default behavior
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77 ==========================================================================
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78 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
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79 bookended intervals into a single, "flattened" or "merged" interval.
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80
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81 ::
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82
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83 $ cat A.bed
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84 chr1 100 200
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85 chr1 180 250
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86 chr1 250 500
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87 chr1 501 1000
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88
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89 $ bedtools merge -i A.bed
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90 chr1 100 500
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91 chr1 501 1000
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92
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93
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94 ==========================================================================
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95 *-s* Enforcing "strandedness"
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96 ==========================================================================
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97 The ``-s`` option will only merge intervals that are overlapping/bookended
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98 *and* are on the same strand.
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99
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100 ::
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101
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102 $ cat A.bed
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103 chr1 100 200 a1 1 +
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104 chr1 180 250 a2 2 +
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105 chr1 250 500 a3 3 -
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106 chr1 501 1000 a4 4 +
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107
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108 $ bedtools merge -i A.bed -s
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109 chr1 100 250 +
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110 chr1 501 1000 +
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111 chr1 250 500 -
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112
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113
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114 ==========================================================================
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115 *-n* Reporting the number of features that were merged
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116 ==========================================================================
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117 The -n option will report the number of features that were combined from the
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118 original file in order to make the newly merged feature. If a feature in the
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119 original file was not merged with any other features, a "1" is reported.
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120
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121 ::
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122
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123 $ cat A.bed
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124 chr1 100 200
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125 chr1 180 250
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126 chr1 250 500
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127 chr1 501 1000
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128
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129 $ bedtools merge -i A.bed -n
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130 chr1 100 500 3
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131 chr1 501 1000 1
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132
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133
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134 ==========================================================================
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135 *-d* Controlling how close two features must be in order to merge
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136 ==========================================================================
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137 By default, only overlapping or book-ended features are combined into a new
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138 feature. However, one can force ``merge`` to combine more distant features
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139 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
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140 features that overlap or are within 1000 base pairs of one another will be
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141 combined.
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142
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143 ::
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144
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145 $ cat A.bed
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146 chr1 100 200
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147 chr1 501 1000
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148
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149 $ bedtools merge -i A.bed
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150 chr1 100 200
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151 chr1 501 1000
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152
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153 $ bedtools merge -i A.bed -d 1000
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154 chr1 100 200 1000
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155
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156
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157 =============================================================
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158 *-nms* Reporting the names of the features that were merged
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159 =============================================================
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160 Occasionally, one might like to know that names of the features that were
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161 merged into a new feature. The ``-nms`` option will add an extra column to the
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162 ``merge`` output which lists (separated by semicolons) the names of the
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163 merged features.
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164
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165 ::
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166
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167 $ cat A.bed
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168 chr1 100 200 A1
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169 chr1 150 300 A2
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170 chr1 250 500 A3
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171
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172 $ bedtools merge -i A.bed -nms
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173 chr1 100 500 A1,A2,A3
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174
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175
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176 ===============================================================
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177 *-scores* Reporting the scores of the features that were merged
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178 ===============================================================
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179 Similarly, we might like to know that scores of the features that were
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180 merged into a new feature. Enter the ``-scores`` option. One can specify
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181 how the scores from each overlapping interval should be reported.
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182
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183 ::
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184
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185 $ cat A.bed
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186 chr1 100 200 A1 1
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187 chr1 150 300 A2 2
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188 chr1 250 500 A3 3
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189
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190 $ bedtools merge -i A.bed -scores mean
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191 chr1 100 500 2
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192
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193 $ bedtools merge -i A.bed -scores max
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194 chr1 100 500 3
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195
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196 $ bedtools merge -i A.bed -scores collapse
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197 chr1 100 500 1,2,3
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198
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199 @REFERENCES@
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200 ]]>
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201 </help>
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202 <expand macro="citations" />
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203 </tool>
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