bedtools: intersectBed.xml annotate

annotate intersectBed.xml @ 30:db1841942d2b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b67e138b17f7e8cb34f59bed0925f691ec9740f3

author	iuc
date	Fri, 17 Aug 2018 05:42:39 -0400
parents	6283d16e40ed
children	4f7a5ccd2ae9

rev	line source
28 6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	1 <tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.2">
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>find overlapping intervals in various ways</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" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	8 <command>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	9 <![CDATA[
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	10 #set modes = ' '.join( str($overlap_mode).split(',') )
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	11
28 6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	12 #if $modes == "None":
6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	13 #set modes = ''
6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	14 #end if
6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	15
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	16 bedtools intersect
13 fadebae7e69b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377 iuc parents: 4 diff changeset	17 #if $inputA.is_of_type('bam'):
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	18 -abam '${inputA}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	19 #else:
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	20 -a '${inputA}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	21 #end if
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	22
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	23 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	24 -b '$reduce_or_iterate.inputB'
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	25 #else:
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	26 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	27 -b '$inputBs'
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	28 #end if
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	29 $split
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	30 $strand
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	31 #if str($fraction) != "None" and str($fraction):
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	32 -f '${fraction}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	33 #end if
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	34 $reciprocal
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	35 $invert
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	36 $once
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	37 $header
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	38 $modes
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	39 $count
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	40 > '${output}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	41 ]]>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	42 </command>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	43 <inputs>
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	44 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A to intersect with B" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	45 <conditional name="reduce_or_iterate">
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	46 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	47 <option value='iterate' selected='true'>One output file per 'input B' file</option>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	48 <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	49 </param>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	50 <when value='iterate'>
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	51 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	52 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	53 </when>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	54 <when value='reduce'>
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	55 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	56 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	57 </when>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	58 </conditional>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	59 <expand macro="strand2" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	60 <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	61 <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	62 <option value="-wb">Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	63 <option value="-wo">Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	64 <option value="-wao">Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by the fraction- and reciprocal option (-wao)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	65 <option value="-loj">Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B (-loj)</option>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	66 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	67
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	68 <expand macro="split" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	69 <!-- -f -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	70 <param name="fraction" type="text"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	71 label="Minimum overlap required as a fraction of the BAM alignment"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	72 help="Alignments are only retained if the overlap with the an interval in the BED file comprises at least this fraction of the BAM alignment's length. For example, to require that the overlap affects 50% of the BAM alignment, use 0.50. (-f)"/>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	73 <!-- -r -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 <expand macro="reciprocal" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	75 <!-- -v -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	76 <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	77 label="Report only those alignments that do not overlap with file(s) B"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	78 help="(-v)"/>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	79 <!-- -u -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	80 <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	81 label="Write the original A entry _once_ if _any_ overlaps found in B."
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	82 help="Just report the fact >=1 hit was found. (-u)" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	83 <!-- -c -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	84 <param name="count" type="boolean" checked="false" truevalue="-c" falsevalue=""
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	85 label="For each entry in A, report the number of overlaps with B."
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	86 help="Reports 0 for A entries that have no overlap with B. (-c)" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	87 <expand macro="print_header" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	88 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	89 <outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	90 <data format_source="inputA" name="output" metadata_source="inputA"/>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	91 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	92 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	93 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	94 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	95 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	96 <param name="overlap_mode" value="-wa" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	97 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	98 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	99 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	100 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	101 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	102 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	103 <param name="overlap_mode" value="-wa,-wb" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	104 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	105 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	106 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	107 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	108 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	109 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	110 <param name="invert" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	111 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	112 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	113 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	114 </tests>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	115 <help>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	116 <![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	117 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	118
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	119 By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both @STD_BEDTOOLS_INPUT_LABEL@ and BAM files as input.
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	120
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	121 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	122
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	123 .. class:: infomark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	124
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	125 Note that each BAM alignment is treated individually. Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	126
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	127 .. class:: infomark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	128
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	129 Note that a BAM alignment will be sent to the output file once even if it overlaps more than one interval in the BED file.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	130
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	131 @REFERENCES@
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	132 ]]>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	133 </help>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	134 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	135 </tool>

Mercurial > repos > iuc > bedtools

annotate intersectBed.xml @ 30:db1841942d2b draft