Mercurial > repos > iuc > bedtools

annotate multiIntersectBed.xml @ 34:dde39ba9c031 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children b28e0cfa7ba1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
1 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
2 <description>identifies common intervals among multiple interval files</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
8 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
9 bedtools multiinter
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 $header
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 $cluster
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 -filler '${filler}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 $empty.empty_selector
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 @GENOME_FILE_UNION@
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
15
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 #if str($tag.tag_select) == "tag":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 -i
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
18 #for $file in $tag.inputs
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 '$file'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 #else:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
22 -i
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 #for $file in $tag.beds:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 '${file.input}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
25 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 -names
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
27 #for $file in $tag.beds:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
28 '{$file.custom_name}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
29 #end for
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
30 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
31 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
32 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
33 <inputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
34 <conditional name="tag">
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <param name="tag_select" type="select" label="Sample name">
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 <option value="tag" selected="true">Use input's tag</option>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
37 <option value="custom">Enter custom name per file</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
38 </param>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
39 <when value="tag">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
40 <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
41 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
42 <when value="custom">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
43 <repeat name="beds" title="Add BED files" min="2" >
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
44 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
45 <param name="custom_name" type="text" area="false" label="Custom sample name" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
46 </repeat>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
47 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
48 </conditional>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
49 <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
50 label="Invoke Ryan Layers's clustering algorithm" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
51 <conditional name="empty">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
52 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
53 <option value="-empty">Yes</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
54 <option value="">No</option>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
55 </param>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
56 <when value="-empty">
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
57 <expand macro="input_conditional_genome_file" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
58 </when>
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
59 <when value="" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
60 </conditional>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
61 <param argument="-filler" type="text" value="N/A"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 label="Text to use for no-coverage value"
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
63 help="Can be 0.0, N/A, - or any other value" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
64 <expand macro="print_header" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
65 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
66 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
67 <data name="output" format="bed" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
68 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
69 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
70 <test>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
71 <param name="tag_select" value="tag" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
72 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
73 <param name="empty_selector" value="" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
74 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
75 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
76 <test>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
77 <param name="tag_select" value="tag" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
78 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
79 <param name="header" value="True" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
80 <param name="empty_selector" value="" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
81 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
82 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
83 <test>
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
84 <param name="tag_select" value="tag" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
85 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
17
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
86 <param name="empty_selector" value="-empty" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
87 <param name="genome_file_opts_selector" value="hist" />
44867b59dbf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
iuc
parents: 11
diff changeset
88 <param name="genome" value="multiIntersectBed1.len" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
89 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
90 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
91 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
92 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
93 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
94
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
95 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
96
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
97
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
98 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
99
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
100 This tool requires that each BED file is reference-sorted (chrom, then start).
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
101
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
102
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
103 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
104
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
105 The output file will contain five fixed columns, plus additional columns for each BED file:
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
106
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
107 * 1. Chromosome name (or 'genome' for whole-genome coverage).
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
108 * 2. The zero-based start position of the interval.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
109 * 3. The one-based end position of the interval.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
110 * 4. The number of input files that had at least one feature overlapping this interval.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
111 * 5. A list of input files or labels that had at least one feature overlapping this interval.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
112 * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
113
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
114 ------
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
115
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
116 **Example input**::
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
117
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
118 # a.bed
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
119 chr1 6 12bed
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
120 chr1 10 20
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
121 chr1 22 27
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
122 chr1 24 30
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
123
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
124 # b.bed
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
125 chr1 12 32
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
126 chr1 14 30
11
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents: 4
diff changeset
127
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
128 # c.bed
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
129 chr1 8 15
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
130 chr1 10 14
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
131 chr1 32 34
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
132
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
133
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
134 ------
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
135
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
136 **Example without a header and without reporting intervals with zero coverage**::
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
137
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
138
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
139 chr1 6 8 1 1 1 0 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
140 chr1 8 12 2 1,3 1 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
141 chr1 12 15 3 1,2,3 1 1 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
142 chr1 15 20 2 1,2 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
143 chr1 20 22 1 2 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
144 chr1 22 30 2 1,2 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
145 chr1 30 32 1 2 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
146 chr1 32 34 1 3 0 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
147
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
148
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
149 **Example adding a header line**::
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
150
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
151
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
152 chrom start end num list a.bed b.bed c.bed
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
153 chr1 6 8 1 1 1 0 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
154 chr1 8 12 2 1,3 1 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
155 chr1 12 15 3 1,2,3 1 1 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
156 chr1 15 20 2 1,2 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
157 chr1 20 22 1 2 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
158 chr1 22 30 2 1,2 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
159 chr1 30 32 1 2 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
160 chr1 32 34 1 3 0 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
161
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
162
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
163 **Example adding a header line and custom file labels**::
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
164
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
165
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
166 chrom start end num list joe bob sue
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
167 chr1 6 8 1 joe 1 0 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
168 chr1 8 12 2 joe,sue 1 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
169 chr1 12 15 3 joe,bob,sue 1 1 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
170 chr1 15 20 2 joe,bob 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
171 chr1 20 22 1 bob 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
172 chr1 22 30 2 joe,bob 1 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
173 chr1 30 32 1 bob 0 1 0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
174 chr1 32 34 1 sue 0 0 1
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
175
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
176
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
177 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
178 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
179 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
180 </tool>