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comparison mergeBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children 38516915ccaf
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9:21f1d1c5467b 10:71af3ebbbb7a
1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1">
2 <description>(mergeBed)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 <![CDATA[
10 mergeBed
11 -i "${input}"
12 $strand
13 -d $distance
14 $header
15 @C_AND_O_ARGUMENT@
16 > "${output}"
17 ]]>
18 </command>
19 <inputs>
20 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
21 <param name="strand" type="select" label="Calculation based on strandedness?">
22 <option value="" selected="True">Overlaps on either strand</option>
23 <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
24 <option value="-S +">Force merge for forward strand only.</option>
25 <option value="-S -">Force merge for reverse strand only.</option>
26 </param>
27 <param name="distance" type="integer" value="0"
28 label="Maximum distance between features allowed for features to be merged"
29 help="That is, overlapping and/or book-ended features are merged. (-d)"/>
30 <expand macro="print_header" />
31 <expand macro="c_and_o_argument" />
32 </inputs>
33 <outputs>
34 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
35 </outputs>
36 <tests>
37 <test>
38 <param name="input" value="mergedBed1.bed" ftype="bed" />
39 <output name="output" file="mergedBed_result1.bed" ftype="bed" />
40 </test>
41 <test>
42 <param name="input" value="mergedBed2.bed" ftype="bed" />
43 <param name="strandedness" value="-s" />
44 <output name="output" file="mergedBed_result2.bed" ftype="bed" />
45 </test>
46 <test>
47 <param name="input" value="mergedBed3.bed" ftype="bed" />
48 <param name="report_number" value="-n" />
49 <output name="output" file="mergedBed_result3.bed" ftype="bed" />
50 </test>
51 <test>
52 <param name="input" value="mergedBed4.bed" ftype="bed" />
53 <param name="distance" value="1000" />
54 <output name="output" file="mergedBed_result4.bed" ftype="bed" />
55 </test>
56 <test>
57 <param name="input" value="mergedBed4.bed" ftype="bed" />
58 <param name="distance" value="1000" />
59 <repeat name="c_and_o_argument_repeat">
60 <param name="col" value="1"/>
61 <param name="operation" value="count"/>
62 </repeat>
63 <output name="output" file="mergedBed_result5.bed" ftype="bed" />
64 </test>
65 </tests>
66 <help>
67 <![CDATA[
68 **What it does**
69
70 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
71
72
73 .. image:: $PATH_TO_IMAGES/merge-glyph.png
74
75
76 .. class:: warningmark
77
78 bedtools merge requires that you presort your data by chromosome and then by start position.
79
80
81 ==========================================================================
82 Default behavior
83 ==========================================================================
84 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
85 bookended intervals into a single, "flattened" or "merged" interval.
86
87 ::
88
89 $ cat A.bed
90 chr1 100 200
91 chr1 180 250
92 chr1 250 500
93 chr1 501 1000
94
95 $ bedtools merge -i A.bed
96 chr1 100 500
97 chr1 501 1000
98
99
100 ==========================================================================
101 *-s* Enforcing "strandedness"
102 ==========================================================================
103 The ``-s`` option will only merge intervals that are overlapping/bookended
104 *and* are on the same strand.
105
106 ::
107
108 $ cat A.bed
109 chr1 100 200 a1 1 +
110 chr1 180 250 a2 2 +
111 chr1 250 500 a3 3 -
112 chr1 501 1000 a4 4 +
113
114 $ bedtools merge -i A.bed -s
115 chr1 100 250 +
116 chr1 501 1000 +
117 chr1 250 500 -
118
119
120 ==========================================================================
121 *-d* Controlling how close two features must be in order to merge
122 ==========================================================================
123 By default, only overlapping or book-ended features are combined into a new
124 feature. However, one can force ``merge`` to combine more distant features
125 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
126 features that overlap or are within 1000 base pairs of one another will be
127 combined.
128
129 ::
130
131 $ cat A.bed
132 chr1 100 200
133 chr1 501 1000
134
135 $ bedtools merge -i A.bed
136 chr1 100 200
137 chr1 501 1000
138
139 $ bedtools merge -i A.bed -d 1000
140 chr1 100 200 1000
141
142
143 @REFERENCES@
144 ]]>
145 </help>
146 <expand macro="citations" />
147 </tool>