bedtools: intersectBed.xml annotate

annotate intersectBed.xml @ 22:bd7721ad15aa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0346e504b5f0aa94215279203beb09b767ada32c

author	iuc
date	Sun, 21 Jan 2018 07:17:19 -0500
parents	df56e1b12d0c
children	95a3b2c25bd1

rev	line source
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	1 <tool id="bedtools_intersectbed" name="Intersect intervals" version="@WRAPPER_VERSION@.1">
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
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	12 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	13 #if $inputA.is_of_type('bam'):
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	14 -abam '${inputA}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	15 #else:
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	16 -a '${inputA}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	17 #end if
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	18
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	19 #if str($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	20 -b '$reduce_or_iterate.inputB'
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	21 #else:
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	22 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	23 -b '$inputBs'
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	24 #end if
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	25 $split
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	26 $strand
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	27 #if str($fraction) != "None" and str($fraction):
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	28 -f '${fraction}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	29 #end if
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	30 $reciprocal
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	31 $invert
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	32 $once
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	33 $header
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	34 $modes
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	35 $count
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	36 > '${output}'
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	37 ]]>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	38 </command>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	39 <inputs>
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	40 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="File A to intersect with B" help="BAM/BED/GFF/VCF format" />
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	41 <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	42 <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	43 <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	44 <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	45 </param>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	46 <when value='iterate'>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	47 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	48 label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	49 </when>
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='reduce'>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	51 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	52 label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
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 </conditional>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	55 <expand macro="strand2" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	56 <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	57 <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	58 <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	59 <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	60 <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	61 <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	62 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	63
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	64 <expand macro="split" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	65 <!-- -f -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	66 <param name="fraction" type="text"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	67 label="Minimum overlap required as a fraction of the BAM alignment"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	68 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	69 <!-- -r -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	70 <expand macro="reciprocal" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	71 <!-- -v -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	72 <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	73 label="Report only those alignments that do not overlap with file(s) B"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 help="(-v)"/>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	75 <!-- -u -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	76 <param name="once" type="boolean" checked="false" truevalue="-u" falsevalue=""
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	77 label="Write the original A entry _once_ if _any_ overlaps found in B."
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	78 help="Just report the fact >=1 hit was found. (-u)" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	79 <!-- -c -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	80 <param name="count" type="boolean" checked="false" truevalue="-c" falsevalue=""
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	81 label="For each entry in A, report the number of overlaps with B."
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	82 help="Reports 0 for A entries that have no overlap with B. (-c)" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	83 <expand macro="print_header" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	84 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	85 <outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	86 <data format_source="inputA" name="output" metadata_source="inputA"/>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	87 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	88 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	89 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	90 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	91 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	92 <param name="overlap_mode" value="-wa" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	93 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	94 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	95 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	96 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	97 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	98 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	99 <param name="overlap_mode" value="-wa,-wb" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	100 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	101 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	102 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	103 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	104 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	105 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	106 <param name="invert" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	107 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	108 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	109 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	110 </tests>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	111 <help>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	112 <![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	113 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	114
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	115 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 BED/GFF/VCF and BAM files as input.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	116
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	117 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	118
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	119 .. class:: infomark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	120
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	121 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	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 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	126
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	127 @REFERENCES@
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	128 ]]>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	129 </help>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	130 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	131 </tool>

Mercurial > repos > iuc > bedtools

annotate intersectBed.xml @ 22:bd7721ad15aa draft