bedtools: intersectBed.xml annotate

annotate intersectBed.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4

author	iuc
date	Sat, 18 May 2024 23:28:38 +0000
parents	07e8b80f278c
children

rev	line source
46 64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4 iuc parents: 43 diff changeset	1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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>
41 7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b" iuc parents: 39 diff changeset	6 <expand macro="bio_tools" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	7 <expand macro="requirements">
46 64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4 iuc parents: 43 diff changeset	8 <requirement type="package" version="1.18">samtools</requirement>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	9 </expand>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	10 <expand macro="stdio" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	11 <command><![CDATA[
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	12 #import re
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	13 #set modes = ' '.join(str($overlap_mode).split(','))
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	14
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	15 #if $modes == "None":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	16 #set modes = ''
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	17 #end if
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	18
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	19 bedtools intersect
37 ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22" iuc parents: 35 diff changeset	20 -a '${inputA}'
28 6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686 iuc parents: 26 diff changeset	21
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	22 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	23 -b '$reduce_or_iterate.inputB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	24 #else:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	25 -b
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	26 #for $file in $reduce_or_iterate.inputB
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	27 '$file'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	28 #end for
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	29
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	30 #if $reduce_or_iterate.names:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	31 #set namesB = "' '".join([re.sub('[^\s\w\-]', '_', str($file.element_identifier)) for $file in $reduce_or_iterate.inputB])
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	32 -names '$namesB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	33 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	34 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	35 $split
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	36 $strand
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	37 #if $fraction_cond.fraction_select == "specify":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	38 #if str($fraction_cond.overlap)
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	39 -f $fraction_cond.overlap
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	40 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	41 $fraction_cond.reciprocal_cond.reciprocal
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	42 #if str($fraction_cond.reciprocal_cond.reciprocal) == '':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	43 #if str($fraction_cond.reciprocal_cond.overlapB):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	44 -F $fraction_cond.reciprocal_cond.overlapB
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	45 #end if
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	46 $fraction_cond.reciprocal_cond.disjoint
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	47 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	48 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	49 $invert
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	50 $once
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	51 $header
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	52 $modes
37 ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22" iuc parents: 35 diff changeset	53 @SORTED@
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	54 @GENOME_FILE@
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	55 $bed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	56 $count
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	57 > '${output}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	58 ]]></command>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	59 <inputs>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	60 <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" 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	61 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	62 <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	63 <option value="iterate" selected="true">One output file per 'input B' file</option>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	64 <option value="reduce">Single output containing intersections of any 'input B' lines with A</option>
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	65 </param>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	66 <when value="iterate">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	67 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	68 label="File 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	69 </when>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	70 <when value="reduce">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	71 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	72 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	73 <param argument="-names" type="boolean" truevalue="yes" falsevalue="no" label="Add data set names instead of indices" />
20 df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	74 </when>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a iuc parents: 13 diff changeset	75 </conditional>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	76 <expand macro="strand2" />
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	77 <param name="overlap_mode" type="select" multiple="true" label="What should be written to the output file?">
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	78 <option value="-wa">Write the original entry in A for each overlap (-wa)</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	79 <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	80 <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	81 <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	82 <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	83 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	84
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	85 <expand macro="split" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	86 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	87 <param name="fraction_select" type="select" label="Required overlap">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	88 <option value="default" selected="true">Default: 1bp</option>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	89 <option value="specify">Specify minimum overlap(s)</option>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	90 </param>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	91 <when value="default"/>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	92 <when value="specify">
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	93 <expand macro="overlap" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	94 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	95 <expand macro="reciprocal" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	96 <when value="-r"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	97 <when value="">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	98 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	99 <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	100 label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	101 </when>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	102 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	103 </when>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	104 </conditional>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	105 <!-- -v -->
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	106 <param name="invert" argument="-v" type="boolean" truevalue="-v" 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	107 label="Report only those alignments that do not overlap with file(s) B" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	108 <!-- -u -->
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	109 <param name="once" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	110 label="Write the original A entry _once_ if _any_ overlaps found in B."
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	111 help="Just report the fact >=1 hit was found" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	112 <!-- -c -->
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	113 <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	114 label="For each entry in A, report the number of overlaps with B."
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	115 help="Reports 0 for A entries that have no overlap with B" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	116 <!-- -bed -->
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	117 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
37 ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22" iuc parents: 35 diff changeset	118 label="When using BAM input, write output as BED instead of BAM." />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	119 <!-- -sorted -g -->
37 ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22" iuc parents: 35 diff changeset	120 <expand macro="sorted" />
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	121 <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	122 <expand macro="print_header" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	123 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	124 <outputs>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	125 <data name="output" format_source="inputA" metadata_source="inputA">
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	126 <change_format>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	127 <when input="bed" value="-bed" format="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	128 </change_format>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	129 </data>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	130 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	131 <tests>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	132 <!-- test adapted from the tutorial https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html -->
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	133 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	134 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	135 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	136 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	137 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	138 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	139 <output name="output" file="intersect-default.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	140 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	141 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	142 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	143 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	144 <param name="reduce_or_iterate_selector" value="reduce" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	145 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	146 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	147 <output name="output" file="intersect-multiple.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	148 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	149 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	150 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	151 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	152 <param name="reduce_or_iterate_selector" value="reduce" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	153 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	154 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	155 <param name="overlap_mode" value="-wa,-wb" />
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	156 <param name="sorted" value="true" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	157 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	158 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	159 <test>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	160 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	161 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	162 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	163 <param name="reduce_or_iterate_selector" value="reduce" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	164 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	165 <param name="names" value="yes" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	166 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	167 <param name="overlap_mode" value="-wa,-wb" />
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	168 <param name="sorted" value="true" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	169 <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	170 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	171 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	172 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	173 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	174 <param name="reduce_or_iterate_selector" value="reduce" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	175 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	176 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	177 <param name="invert" value="-v" />
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	178 <param name="sorted" value="true" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	179 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	180 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	181 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	182 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	183 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	184 <param name="reduce_or_iterate_selector" value="reduce" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	185 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	186 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	187 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	188 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	189 <param name="fraction_select" value="specify"/>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	190 <param name="overlap" value="1.0" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	191 </conditional>
43 07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f" iuc parents: 41 diff changeset	192 <param name="sorted" value="true" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	193 <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	194 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	195 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	196 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	197 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	198 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	199 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	200 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	201 <param name="overlap_mode" value="-wa" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	202 <output name="output" file="intersect-wa.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	203 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	204 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	205 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	206 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	207 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	208 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	209 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	210 <param name="overlap_mode" value="-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	211 <output name="output" file="intersect-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	212 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	213 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	214 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	215 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	216 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	217 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	218 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	219 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	220 <output name="output" file="intersect-wa-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	221 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	222 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	223 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	224 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	225 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	226 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	227 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	228 <param name="overlap_mode" value="-loj" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	229 <output name="output" file="intersect-loj.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	230 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	231 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	232 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	233 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	234 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	235 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	236 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	237 <param name="overlap_mode" value="-wo" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	238 <output name="output" file="intersect-wo.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	239 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	240 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	241 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	242 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	243 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	244 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	245 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	246 <param name="overlap_mode" value="-wao" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	247 <output name="output" file="intersect-wao.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	248 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	249 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	250 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	251 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	252 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	253 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	254 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	255 <param name="once" value="-u" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	256 <output name="output" file="intersect-unique.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	257 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	258 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	259 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	260 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	261 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	262 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	263 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	264 <param name="count" value="-c"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	265 <output name="output" file="intersect-count.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	266 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	267 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	268 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	269 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	270 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	271 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	272 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	273 <param name="invert" value="-v"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	274 <output name="output" file="intersect-invert.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	275 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	276 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	277 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	278 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	279 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	280 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	281 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	282 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	283 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	284 <param name="fraction_select" value="specify"/>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	285 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	286 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	287 <output name="output" file="intersect-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	288 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	289 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	290 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	291 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	292 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	293 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	294 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	295 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	296 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	297 <param name="fraction_select" value="specify"/>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	298 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	299 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	300 <param name="reciprocal" value="-r" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	301 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	302 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	303 <output name="output" file="intersect-fracA-rec.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	304 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	305 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	306 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	307 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	308 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	309 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	310 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	311 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	312 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	313 <param name="fraction_select" value="specify"/>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	314 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	315 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	316 <param name="overlapB" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	317 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	318 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	319 <output name="output" file="intersect-fracA-rec.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	320 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	321 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	322 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	323 <conditional name="reduce_or_iterate">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	324 <param name="reduce_or_iterate_selector" value="iterate" />
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	325 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	326 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	327 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	328 <conditional name="fraction_cond">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	329 <param name="fraction_select" value="specify"/>
32 4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	330 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	331 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	332 <param name="overlapB" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	333 <param name="disjoint" value="-e" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	334 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	335 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	336 <output name="output" file="intersect-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	337 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74 iuc parents: 28 diff changeset	338 <!-- old tests -->
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	339 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	340 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	341 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	342 <param name="overlap_mode" value="-wa" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	343 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	344 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	345 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	346 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	347 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	348 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	349 <param name="overlap_mode" value="-wa,-wb" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	350 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	351 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	352 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	353 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	354 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	355 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	356 <param name="invert" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	357 <param name="split" value="False" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	358 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	359 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	360 </tests>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	361 <help><![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	362 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	363
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 20 diff changeset	364 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	365
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	366 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	367
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	368 .. class:: infomark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	369
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	370 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	371
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	372 .. class:: infomark
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	373
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	374 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	375
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	376 @REFERENCES@
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	377 ]]></help>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	378 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	379 </tool>

Mercurial > repos > iuc > bedtools

annotate intersectBed.xml @ 46:64e2edfe7a2c draft default tip