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comparison mergeBed.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0">
2 <description>(mergeBed)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 mergeBed
10 -i $input
11 $strandedness
12 $report_number
13 -d $distance
14 $nms
15 #if str($scores) != 'none'
16 -scores $scores
17 #end if
18 &gt; $output
19 </command>
20 <inputs>
21 <param name="input" format="bed,gff,vcf" type="data" label="Sort the following BED/VCF/GFF file"/>
22 <param name="strandedness" type="boolean" label="Force strandedness." truevalue="-s" falsevalue="" checked="false"
23 help="That is, only merge features that are the same strand."/>
24 <param name="report_number" type="boolean" label="Report the number of BED entries that were merged." truevalue="-n" falsevalue="" checked="false"
25 help="1 is reported if no merging occurred."/>
26 <param name="nms" type="boolean" label="Report the names of the merged features separated by commas." truevalue="-nms" falsevalue="" checked="false"
27 help="1 is reported if no merging occurred."/>
28
29 <param name="distance" type="integer" value="0" label="Maximum distance between features allowed for features to be merged."
30 help="That is, overlapping and/or book-ended features are merged."/>
31 <param name="scores" type="select" label="Report the scores of the merged features as">
32 <option value="none" selected="True">Do not report at all</option>
33 <option value="sum">Sum</option>
34 <expand macro="math_options" />
35 </param>
36 </inputs>
37 <outputs>
38 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="input" value="0.bed" ftype="bed" />
43 <output name="output" file="0_result.bed" ftype="bed" />
44 </test>
45 <test>
46 <param name="input" value="1.bed" ftype="bed" />
47 <param name="strandedness" value="-s" />
48 <output name="output" file="1_result.bed" ftype="bed" />
49 </test>
50 <test>
51 <param name="input" value="2.bed" ftype="bed" />
52 <param name="report_number" value="-n" />
53 <output name="output" file="2_result.bed" ftype="bed" />
54 </test>
55 <test>
56 <param name="input" value="3.bed" ftype="bed" />
57 <param name="distance" value="1000" />
58 <output name="output" file="3_result.bed" ftype="bed" />
59 </test>
60 </tests>
61 <help>
62
63 **What it does**
64
65 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
66
67
68 .. image:: $PATH_TO_IMAGES/merge-glyph.png
69
70
71 .. class:: warningmark
72
73 bedtools merge requires that you presort your data by chromosome and then by start position.
74
75
76 ==========================================================================
77 Default behavior
78 ==========================================================================
79 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
80 bookended intervals into a single, "flattened" or "merged" interval.
81
82 ::
83
84 $ cat A.bed
85 chr1 100 200
86 chr1 180 250
87 chr1 250 500
88 chr1 501 1000
89
90 $ bedtools merge -i A.bed
91 chr1 100 500
92 chr1 501 1000
93
94
95 ==========================================================================
96 *-s* Enforcing "strandedness"
97 ==========================================================================
98 The ``-s`` option will only merge intervals that are overlapping/bookended
99 *and* are on the same strand.
100
101 ::
102
103 $ cat A.bed
104 chr1 100 200 a1 1 +
105 chr1 180 250 a2 2 +
106 chr1 250 500 a3 3 -
107 chr1 501 1000 a4 4 +
108
109 $ bedtools merge -i A.bed -s
110 chr1 100 250 +
111 chr1 501 1000 +
112 chr1 250 500 -
113
114
115 ==========================================================================
116 *-n* Reporting the number of features that were merged
117 ==========================================================================
118 The -n option will report the number of features that were combined from the
119 original file in order to make the newly merged feature. If a feature in the
120 original file was not merged with any other features, a "1" is reported.
121
122 ::
123
124 $ cat A.bed
125 chr1 100 200
126 chr1 180 250
127 chr1 250 500
128 chr1 501 1000
129
130 $ bedtools merge -i A.bed -n
131 chr1 100 500 3
132 chr1 501 1000 1
133
134
135 ==========================================================================
136 *-d* Controlling how close two features must be in order to merge
137 ==========================================================================
138 By default, only overlapping or book-ended features are combined into a new
139 feature. However, one can force ``merge`` to combine more distant features
140 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
141 features that overlap or are within 1000 base pairs of one another will be
142 combined.
143
144 ::
145
146 $ cat A.bed
147 chr1 100 200
148 chr1 501 1000
149
150 $ bedtools merge -i A.bed
151 chr1 100 200
152 chr1 501 1000
153
154 $ bedtools merge -i A.bed -d 1000
155 chr1 100 200 1000
156
157
158 =============================================================
159 *-nms* Reporting the names of the features that were merged
160 =============================================================
161 Occasionally, one might like to know that names of the features that were
162 merged into a new feature. The ``-nms`` option will add an extra column to the
163 ``merge`` output which lists (separated by semicolons) the names of the
164 merged features.
165
166 ::
167
168 $ cat A.bed
169 chr1 100 200 A1
170 chr1 150 300 A2
171 chr1 250 500 A3
172
173 $ bedtools merge -i A.bed -nms
174 chr1 100 500 A1,A2,A3
175
176
177 ===============================================================
178 *-scores* Reporting the scores of the features that were merged
179 ===============================================================
180 Similarly, we might like to know that scores of the features that were
181 merged into a new feature. Enter the ``-scores`` option. One can specify
182 how the scores from each overlapping interval should be reported.
183
184 ::
185
186 $ cat A.bed
187 chr1 100 200 A1 1
188 chr1 150 300 A2 2
189 chr1 250 500 A3 3
190
191 $ bedtools merge -i A.bed -scores mean
192 chr1 100 500 2
193
194 $ bedtools merge -i A.bed -scores max
195 chr1 100 500 3
196
197 $ bedtools merge -i A.bed -scores collapse
198 chr1 100 500 1,2,3
199
200
201 @REFERENCES@
202 </help>
203 </tool>