bedtools: multiIntersectBed.xml annotate

annotate multiIntersectBed.xml @ 56:7a06bb42dbb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

author	iuc
date	Tue, 31 Aug 2021 07:45:56 +0000
parents	9a9f1a7abf54
children	1d0a0d6a78b1

rev	line source
52 9a9f1a7abf54 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5" iuc parents: 50 diff changeset	1 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@">
17 a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 8 diff changeset	2 <description>identifies common intervals among multiple interval files</description>
56 7a06bb42dbb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 52 diff changeset	3 <expand macro="bio_tools" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	4 <macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	5 <import>macros.xml</import>
0d3aa592ce27 Uploaded iuc parents: diff changeset	6 </macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	7 <expand macro="requirements" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	8 <expand macro="stdio" />
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	10 bedtools multiinter
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	11 $header
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	12 $cluster
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	13 -filler '${filler}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	14 $empty.empty_selector
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	15 @GENOME_FILE_UNION@
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	16
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	17 #if str($tag.tag_select) == "tag":
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	18 -i
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	19 #for $file in $tag.inputs
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	20 '$file'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	21 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	22 #else:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	23 -i
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	24 #for $file in $tag.beds:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	25 '${file.input}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	26 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	27 -names
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	28 #for $file in $tag.beds:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	29 '{$file.custom_name}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	30 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	31 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	32 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	33 ]]></command>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	34 <inputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	35 <conditional name="tag">
0d3aa592ce27 Uploaded iuc parents: diff changeset	36 <param name="tag_select" type="select" label="Sample name">
0d3aa592ce27 Uploaded iuc parents: diff changeset	37 <option value="tag" selected="true">Use input's tag</option>
0d3aa592ce27 Uploaded iuc parents: diff changeset	38 <option value="custom">Enter custom name per file</option>
0d3aa592ce27 Uploaded iuc parents: diff changeset	39 </param>
0d3aa592ce27 Uploaded iuc parents: diff changeset	40 <when value="tag">
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	41 <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	42 </when>
0d3aa592ce27 Uploaded iuc parents: diff changeset	43 <when value="custom">
0d3aa592ce27 Uploaded iuc parents: diff changeset	44 <repeat name="beds" title="Add BED files" min="2" >
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	45 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	46 <param name="custom_name" type="text" area="false" label="Custom sample name" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	47 </repeat>
0d3aa592ce27 Uploaded iuc parents: diff changeset	48 </when>
0d3aa592ce27 Uploaded iuc parents: diff changeset	49 </conditional>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	50 <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	51 label="Invoke Ryan Layers's clustering algorithm" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	52 <conditional name="empty">
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	53 <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	54 <option value="-empty">Yes</option>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	55 <option value="">No</option>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	56 </param>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	57 <when value="-empty">
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	58 <expand macro="input_conditional_genome_file" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	59 </when>
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	60 <when value="" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	61 </conditional>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	62 <param argument="-filler" type="text" value="N/A"
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	63 label="Text to use for no-coverage value"
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	64 help="Can be 0.0, N/A, - or any other value" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	65 <expand macro="print_header" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	66 </inputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	67 <outputs>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	68 <data name="output" format="bed" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	69 </outputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	70 <tests>
0d3aa592ce27 Uploaded iuc parents: diff changeset	71 <test>
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	72 <param name="tag_select" value="tag" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	73 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	74 <param name="empty_selector" value="" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	75 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	76 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	77 <test>
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	78 <param name="tag_select" value="tag" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	79 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	80 <param name="header" value="True" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	81 <param name="empty_selector" value="" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	82 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	83 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	84 <test>
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	85 <param name="tag_select" value="tag" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	86 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
32 b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	87 <param name="empty_selector" value="-empty" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	88 <param name="genome_file_opts_selector" value="hist" />
b0d5e752c0c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348 iuc parents: 26 diff changeset	89 <param name="genome" value="multiIntersectBed1.len" />
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	90 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	91 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	92 </tests>
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	93 <help><![CDATA[
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	94 What it does
0d3aa592ce27 Uploaded iuc parents: diff changeset	95
0d3aa592ce27 Uploaded iuc parents: diff changeset	96 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
0d3aa592ce27 Uploaded iuc parents: diff changeset	97
0d3aa592ce27 Uploaded iuc parents: diff changeset	98
0d3aa592ce27 Uploaded iuc parents: diff changeset	99 .. class:: warningmark
0d3aa592ce27 Uploaded iuc parents: diff changeset	100
0d3aa592ce27 Uploaded iuc parents: diff changeset	101 This tool requires that each BED file is reference-sorted (chrom, then start).
0d3aa592ce27 Uploaded iuc parents: diff changeset	102
0d3aa592ce27 Uploaded iuc parents: diff changeset	103
0d3aa592ce27 Uploaded iuc parents: diff changeset	104 .. class:: infomark
0d3aa592ce27 Uploaded iuc parents: diff changeset	105
0d3aa592ce27 Uploaded iuc parents: diff changeset	106 The output file will contain five fixed columns, plus additional columns for each BED file:
0d3aa592ce27 Uploaded iuc parents: diff changeset	107
0d3aa592ce27 Uploaded iuc parents: diff changeset	108 * 1. Chromosome name (or 'genome' for whole-genome coverage).
0d3aa592ce27 Uploaded iuc parents: diff changeset	109 * 2. The zero-based start position of the interval.
0d3aa592ce27 Uploaded iuc parents: diff changeset	110 * 3. The one-based end position of the interval.
0d3aa592ce27 Uploaded iuc parents: diff changeset	111 * 4. The number of input files that had at least one feature overlapping this interval.
0d3aa592ce27 Uploaded iuc parents: diff changeset	112 * 5. A list of input files or labels that had at least one feature overlapping this interval.
0d3aa592ce27 Uploaded iuc parents: diff changeset	113 * 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	114
0d3aa592ce27 Uploaded iuc parents: diff changeset	115 ------
0d3aa592ce27 Uploaded iuc parents: diff changeset	116
0d3aa592ce27 Uploaded iuc parents: diff changeset	117 Example input::
0d3aa592ce27 Uploaded iuc parents: diff changeset	118
0d3aa592ce27 Uploaded iuc parents: diff changeset	119 # a.bed
0d3aa592ce27 Uploaded iuc parents: diff changeset	120 chr1 6 12bed
0d3aa592ce27 Uploaded iuc parents: diff changeset	121 chr1 10 20
0d3aa592ce27 Uploaded iuc parents: diff changeset	122 chr1 22 27
0d3aa592ce27 Uploaded iuc parents: diff changeset	123 chr1 24 30
26 c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 17 diff changeset	124
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	125 # b.bed
0d3aa592ce27 Uploaded iuc parents: diff changeset	126 chr1 12 32
0d3aa592ce27 Uploaded iuc parents: diff changeset	127 chr1 14 30
26 c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811 iuc parents: 17 diff changeset	128
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	129 # c.bed
0d3aa592ce27 Uploaded iuc parents: diff changeset	130 chr1 8 15
0d3aa592ce27 Uploaded iuc parents: diff changeset	131 chr1 10 14
0d3aa592ce27 Uploaded iuc parents: diff changeset	132 chr1 32 34
0d3aa592ce27 Uploaded iuc parents: diff changeset	133
0d3aa592ce27 Uploaded iuc parents: diff changeset	134
0d3aa592ce27 Uploaded iuc parents: diff changeset	135 ------
0d3aa592ce27 Uploaded iuc parents: diff changeset	136
0d3aa592ce27 Uploaded iuc parents: diff changeset	137 Example without a header and without reporting intervals with zero coverage::
0d3aa592ce27 Uploaded iuc parents: diff changeset	138
0d3aa592ce27 Uploaded iuc parents: diff changeset	139
0d3aa592ce27 Uploaded iuc parents: diff changeset	140 chr1 6 8 1 1 1 0 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	141 chr1 8 12 2 1,3 1 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	142 chr1 12 15 3 1,2,3 1 1 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	143 chr1 15 20 2 1,2 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	144 chr1 20 22 1 2 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	145 chr1 22 30 2 1,2 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	146 chr1 30 32 1 2 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	147 chr1 32 34 1 3 0 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	148
0d3aa592ce27 Uploaded iuc parents: diff changeset	149
0d3aa592ce27 Uploaded iuc parents: diff changeset	150 Example adding a header line::
0d3aa592ce27 Uploaded iuc parents: diff changeset	151
0d3aa592ce27 Uploaded iuc parents: diff changeset	152
0d3aa592ce27 Uploaded iuc parents: diff changeset	153 chrom start end num list a.bed b.bed c.bed
0d3aa592ce27 Uploaded iuc parents: diff changeset	154 chr1 6 8 1 1 1 0 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	155 chr1 8 12 2 1,3 1 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	156 chr1 12 15 3 1,2,3 1 1 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	157 chr1 15 20 2 1,2 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	158 chr1 20 22 1 2 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	159 chr1 22 30 2 1,2 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	160 chr1 30 32 1 2 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	161 chr1 32 34 1 3 0 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	162
0d3aa592ce27 Uploaded iuc parents: diff changeset	163
0d3aa592ce27 Uploaded iuc parents: diff changeset	164 Example adding a header line and custom file labels::
0d3aa592ce27 Uploaded iuc parents: diff changeset	165
0d3aa592ce27 Uploaded iuc parents: diff changeset	166
0d3aa592ce27 Uploaded iuc parents: diff changeset	167 chrom start end num list joe bob sue
0d3aa592ce27 Uploaded iuc parents: diff changeset	168 chr1 6 8 1 joe 1 0 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	169 chr1 8 12 2 joe,sue 1 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	170 chr1 12 15 3 joe,bob,sue 1 1 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	171 chr1 15 20 2 joe,bob 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	172 chr1 20 22 1 bob 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	173 chr1 22 30 2 joe,bob 1 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	174 chr1 30 32 1 bob 0 1 0
0d3aa592ce27 Uploaded iuc parents: diff changeset	175 chr1 32 34 1 sue 0 0 1
0d3aa592ce27 Uploaded iuc parents: diff changeset	176
0d3aa592ce27 Uploaded iuc parents: diff changeset	177
0d3aa592ce27 Uploaded iuc parents: diff changeset	178 @REFERENCES@
50 df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 48 diff changeset	179 ]]></help>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	180 <expand macro="citations" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	181 </tool>

Mercurial > repos > iuc > bedtools

annotate multiIntersectBed.xml @ 56:7a06bb42dbb1 draft