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1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
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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 $header
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15 @C_AND_O_ARGUMENT@
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16 > "${output}"
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
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21 <param name="strand" type="select" label="Calculation based on strandedness?">
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22 <option value="" selected="True">Overlaps on either strand</option>
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23 <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
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24 <option value="-S +">Force merge for forward strand only.</option>
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25 <option value="-S -">Force merge for reverse strand only.</option>
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26 </param>
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27 <param name="distance" type="integer" value="0"
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28 label="Maximum distance between features allowed for features to be merged"
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29 help="That is, overlapping and/or book-ended features are merged. (-d)"/>
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30 <expand macro="print_header" />
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3
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31 <expand macro="c_and_o_argument">
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32 <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
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33 </expand>
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34 </inputs>
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35 <outputs>
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36 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" value="mergedBed1.bed" ftype="bed" />
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41 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
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42 </test>
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43 <test>
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44 <param name="input" value="mergedBed2.bed" ftype="bed" />
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45 <param name="strandedness" value="-s" />
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46 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
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47 </test>
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48 <test>
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49 <param name="input" value="mergedBed3.bed" ftype="bed" />
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50 <param name="report_number" value="-n" />
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51 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
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52 </test>
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53 <test>
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54 <param name="input" value="mergedBed4.bed" ftype="bed" />
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55 <param name="distance" value="1000" />
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56 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
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57 </test>
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58 <test>
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59 <param name="input" value="mergedBed4.bed" ftype="bed" />
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60 <param name="distance" value="1000" />
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61 <repeat name="c_and_o_argument_repeat">
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62 <param name="col" value="1"/>
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63 <param name="operation" value="count"/>
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64 </repeat>
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65 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
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66 </test>
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67 </tests>
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68 <help>
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69 <![CDATA[
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70 **What it does**
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71
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72 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
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74
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75 .. image:: $PATH_TO_IMAGES/merge-glyph.png
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76
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77
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78 .. class:: warningmark
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79
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80 bedtools merge requires that you presort your data by chromosome and then by start position.
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81
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82
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83 ==========================================================================
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84 Default behavior
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85 ==========================================================================
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86 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
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87 bookended intervals into a single, "flattened" or "merged" interval.
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88
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89 ::
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90
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91 $ cat A.bed
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92 chr1 100 200
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93 chr1 180 250
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94 chr1 250 500
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95 chr1 501 1000
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96
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97 $ bedtools merge -i A.bed
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98 chr1 100 500
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99 chr1 501 1000
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100
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101
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102 ==========================================================================
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103 *-s* Enforcing "strandedness"
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104 ==========================================================================
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105 The ``-s`` option will only merge intervals that are overlapping/bookended
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106 *and* are on the same strand.
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107
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108 ::
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109
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110 $ cat A.bed
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111 chr1 100 200 a1 1 +
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112 chr1 180 250 a2 2 +
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113 chr1 250 500 a3 3 -
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114 chr1 501 1000 a4 4 +
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115
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116 $ bedtools merge -i A.bed -s
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117 chr1 100 250 +
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118 chr1 501 1000 +
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119 chr1 250 500 -
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120
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121
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122 ==========================================================================
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123 *-d* Controlling how close two features must be in order to merge
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124 ==========================================================================
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125 By default, only overlapping or book-ended features are combined into a new
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126 feature. However, one can force ``merge`` to combine more distant features
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127 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
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128 features that overlap or are within 1000 base pairs of one another will be
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129 combined.
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130
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131 ::
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132
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133 $ cat A.bed
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134 chr1 100 200
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135 chr1 501 1000
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136
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137 $ bedtools merge -i A.bed
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138 chr1 100 200
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139 chr1 501 1000
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140
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141 $ bedtools merge -i A.bed -d 1000
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142 chr1 100 200 1000
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143
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144
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145 @REFERENCES@
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146 ]]>
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147 </help>
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148 <expand macro="citations" />
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149 </tool>
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