bedtools: intersectBed.xml annotate

annotate intersectBed.xml @ 44:9224d51be786 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686

author	iuc
date	Sun, 24 Jun 2018 11:52:19 -0400
parents	d279800f4ff9
children	2f457890d8c8

rev	line source
44 9224d51be786 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 42 diff changeset	1 <tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.2">
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>find overlapping intervals in various ways</description>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	3 <macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	4 <import>macros.xml</import>
0d3aa592ce27 Uploaded iuc parents: diff changeset	5 </macros>
0d3aa592ce27 Uploaded iuc parents: diff changeset	6 <expand macro="requirements" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	7 <expand macro="stdio" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	8 <command>
0d3aa592ce27 Uploaded iuc parents: diff changeset	9 <![CDATA[
0d3aa592ce27 Uploaded iuc parents: diff changeset	10 #set modes = ' '.join( str($overlap_mode).split(',') )
0d3aa592ce27 Uploaded iuc parents: diff changeset	11
44 9224d51be786 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 42 diff changeset	12 #if $modes == "None":
9224d51be786 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 42 diff changeset	13 #set modes = ''
9224d51be786 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 42 diff changeset	14 #end if
9224d51be786 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 42 diff changeset	15
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	16 bedtools intersect
28 f0aca67fdb71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377 iuc parents: 18 diff changeset	17 #if $inputA.is_of_type('bam'):
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	18 -abam '${inputA}'
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	19 #else:
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	20 -a '${inputA}'
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	21 #end if
0d3aa592ce27 Uploaded iuc parents: diff changeset	22
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	23 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	24 -b '$reduce_or_iterate.inputB'
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	25 #else:
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	26 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	27 -b '$inputBs'
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	28 #end if
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	29 $split
0d3aa592ce27 Uploaded iuc parents: diff changeset	30 $strand
0d3aa592ce27 Uploaded iuc parents: diff changeset	31 #if str($fraction) != "None" and str($fraction):
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	32 -f '${fraction}'
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	33 #end if
0d3aa592ce27 Uploaded iuc parents: diff changeset	34 $reciprocal
0d3aa592ce27 Uploaded iuc parents: diff changeset	35 $invert
0d3aa592ce27 Uploaded iuc parents: diff changeset	36 $once
0d3aa592ce27 Uploaded iuc parents: diff changeset	37 $header
0d3aa592ce27 Uploaded iuc parents: diff changeset	38 $modes
18 5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 17 diff changeset	39 $count
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	40 > '${output}'
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	41 ]]>
0d3aa592ce27 Uploaded iuc parents: diff changeset	42 </command>
0d3aa592ce27 Uploaded iuc parents: diff changeset	43 <inputs>
42 d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 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" />
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	45 <conditional name="reduce_or_iterate">
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	46 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	47 <option value='iterate' selected='true'>One output file per 'input B' file</option>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	48 <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	49 </param>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	50 <when value='iterate'>
42 d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 diff changeset	51 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 diff changeset	52 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	53 </when>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	54 <when value='reduce'>
42 d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 diff changeset	55 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 diff changeset	56 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	57 </when>
1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	58 </conditional>
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	59 <expand macro="strand2" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	60 <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
0d3aa592ce27 Uploaded iuc parents: diff changeset	61 <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
0d3aa592ce27 Uploaded iuc parents: 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>
0d3aa592ce27 Uploaded iuc parents: 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>
0d3aa592ce27 Uploaded iuc parents: 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>
0d3aa592ce27 Uploaded iuc parents: 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>
0d3aa592ce27 Uploaded iuc parents: diff changeset	66 </param>
0d3aa592ce27 Uploaded iuc parents: diff changeset	67
0d3aa592ce27 Uploaded iuc parents: diff changeset	68 <expand macro="split" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	69 <!-- -f -->
0d3aa592ce27 Uploaded iuc parents: diff changeset	70 <param name="fraction" type="text"
0d3aa592ce27 Uploaded iuc parents: diff changeset	71 label="Minimum overlap required as a fraction of the BAM alignment"
0d3aa592ce27 Uploaded iuc parents: 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)"/>
0d3aa592ce27 Uploaded iuc parents: diff changeset	73 <!-- -r -->
0d3aa592ce27 Uploaded iuc parents: diff changeset	74 <expand macro="reciprocal" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	75 <!-- -v -->
0d3aa592ce27 Uploaded iuc parents: diff changeset	76 <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue=""
36 1133660b0f9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 28 diff changeset	77 label="Report only those alignments that do not overlap with file(s) B"
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	78 help="(-v)"/>
0d3aa592ce27 Uploaded iuc parents: diff changeset	79 <!-- -u -->
0d3aa592ce27 Uploaded iuc parents: diff changeset	80 <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
0d3aa592ce27 Uploaded iuc parents: diff changeset	81 label="Write the original A entry _once_ if _any_ overlaps found in B."
0d3aa592ce27 Uploaded iuc parents: diff changeset	82 help="Just report the fact >=1 hit was found. (-u)" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	83 <!-- -c -->
0d3aa592ce27 Uploaded iuc parents: diff changeset	84 <param name="count" type="boolean" checked="false" truevalue="-c" falsevalue=""
0d3aa592ce27 Uploaded iuc parents: diff changeset	85 label="For each entry in A, report the number of overlaps with B."
0d3aa592ce27 Uploaded iuc parents: diff changeset	86 help="Reports 0 for A entries that have no overlap with B. (-c)" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	87 <expand macro="print_header" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	88 </inputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	89 <outputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	90 <data format_source="inputA" name="output" metadata_source="inputA"/>
0d3aa592ce27 Uploaded iuc parents: diff changeset	91 </outputs>
0d3aa592ce27 Uploaded iuc parents: diff changeset	92 <tests>
0d3aa592ce27 Uploaded iuc parents: diff changeset	93 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	94 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	95 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	96 <param name="overlap_mode" value="-wa" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	97 <param name="split" value="False" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	98 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	99 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	100 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	101 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	102 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	103 <param name="overlap_mode" value="-wa,-wb" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	104 <param name="split" value="False" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	105 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	106 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	107 <test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	108 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	109 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	110 <param name="invert" value="True" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	111 <param name="split" value="False" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	112 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	113 </test>
0d3aa592ce27 Uploaded iuc parents: diff changeset	114 </tests>
0d3aa592ce27 Uploaded iuc parents: diff changeset	115 <help>
0d3aa592ce27 Uploaded iuc parents: diff changeset	116 <![CDATA[
0d3aa592ce27 Uploaded iuc parents: diff changeset	117 What it does
0d3aa592ce27 Uploaded iuc parents: diff changeset	118
42 d279800f4ff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 36 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.
8 0d3aa592ce27 Uploaded iuc parents: diff changeset	120
0d3aa592ce27 Uploaded iuc parents: diff changeset	121 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
0d3aa592ce27 Uploaded iuc parents: diff changeset	122
0d3aa592ce27 Uploaded iuc parents: diff changeset	123 .. class:: infomark
0d3aa592ce27 Uploaded iuc parents: diff changeset	124
0d3aa592ce27 Uploaded 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	126
0d3aa592ce27 Uploaded iuc parents: diff changeset	127 .. class:: infomark
0d3aa592ce27 Uploaded iuc parents: diff changeset	128
0d3aa592ce27 Uploaded 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.
0d3aa592ce27 Uploaded iuc parents: diff changeset	130
0d3aa592ce27 Uploaded iuc parents: diff changeset	131 @REFERENCES@
0d3aa592ce27 Uploaded iuc parents: diff changeset	132 ]]>
0d3aa592ce27 Uploaded iuc parents: diff changeset	133 </help>
0d3aa592ce27 Uploaded iuc parents: diff changeset	134 <expand macro="citations" />
0d3aa592ce27 Uploaded iuc parents: diff changeset	135 </tool>

Mercurial > repos > iuc > bedtools

annotate intersectBed.xml @ 44:9224d51be786 draft