| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.19.0 |
| bedtools_intersectbed |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bedtools | 2.30.0 | package |
| samtools | 1.9 | package |
| Additional information about this tool |
#import re
#set modes = ' '.join(str($overlap_mode).split(','))
#if $modes == "None":
#set modes = ''
#end if
bedtools intersect
-a '${inputA}'
#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
-b '$reduce_or_iterate.inputB'
#else:
-b
#for $file in $reduce_or_iterate.inputB
'$file'
#end for
#if $reduce_or_iterate.names:
#set namesB = "' '".join([re.sub('[^\s\w\-]', '_', str($file.element_identifier)) for $file in $reduce_or_iterate.inputB])
-names '$namesB'
#end if
#end if
$split
$strand
#if $fraction_cond.fraction_select == "specify":
#if str($fraction_cond.overlap)
-f $fraction_cond.overlap
#end if
$fraction_cond.reciprocal_cond.reciprocal
#if str($fraction_cond.reciprocal_cond.reciprocal) == '':
#if str($fraction_cond.reciprocal_cond.overlapB):
-F $fraction_cond.reciprocal_cond.overlapB
#end if
$fraction_cond.reciprocal_cond.disjoint
#end if
#end if
$invert
$once
$header
$modes
$sorted
#if str($sorted) != '':
#if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
-g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
#else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
-g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
#end if
#end if
#if $genome_file_opts.genome
-g
#if $genome_file_opts.genome_file_opts_selector == "loc":
'$genome_file_opts.genome.fields.len_path'
#elif $genome_file_opts.genome_file_opts_selector == "hist":
'$genome_file_opts.genome'
#end if
#end if
$bed
$count
> '${output}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-2 |
inputA: intersect-query.bed reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] reduce_or_iterate|reduce_or_iterate_selector: reduce |
name: value |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed value |
| Test-3 |
inputA: intersect-query.bed reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] reduce_or_iterate|reduce_or_iterate_selector: reduce overlap_mode: ['-wa', '-wb'] sorted: True |
name: value |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed value |
| Test-4 |
inputA: intersect-query.bed reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] reduce_or_iterate|names: True reduce_or_iterate|reduce_or_iterate_selector: reduce overlap_mode: ['-wa', '-wb'] sorted: True |
name: value |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed value |
| Test-5 |
inputA: intersect-query.bed reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] reduce_or_iterate|reduce_or_iterate_selector: reduce invert: True sorted: True |
name: value |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed value |
| Test-6 |
inputA: intersect-query.bed reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] reduce_or_iterate|reduce_or_iterate_selector: reduce overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 1.0 fraction_cond|fraction_select: specify sorted: True |
name: value |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed value |
| Test-7 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: -wa |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-8 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: -wb |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-9 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: ['-wa', '-wb'] |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-10 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: -loj |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-11 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: -wo |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-12 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: -wao |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-13 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate once: True |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-14 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate count: True |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-15 |
inputA: intersect-A.bed reduce_or_iterate|inputB: intersect-B.bed reduce_or_iterate|reduce_or_iterate_selector: iterate invert: True |
name: value |
intersect-A.bed intersect-B.bed value |
| Test-16 |
inputA: intersect-A2.bed reduce_or_iterate|inputB: intersect-B2.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|fraction_select: specify |
name: value |
intersect-A2.bed intersect-B2.bed value |
| Test-17 |
inputA: intersect-A2.bed reduce_or_iterate|inputB: intersect-B2.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|reciprocal_cond|reciprocal: -r fraction_cond|fraction_select: specify |
name: value |
intersect-A2.bed intersect-B2.bed value |
| Test-18 |
inputA: intersect-A2.bed reduce_or_iterate|inputB: intersect-B2.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|reciprocal_cond|overlapB: 0.5 fraction_cond|fraction_select: specify |
name: value |
intersect-A2.bed intersect-B2.bed value |
| Test-19 |
inputA: intersect-A2.bed reduce_or_iterate|inputB: intersect-B2.bed reduce_or_iterate|reduce_or_iterate_selector: iterate overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|reciprocal_cond|overlapB: 0.5 fraction_cond|reciprocal_cond|disjoint: True fraction_cond|fraction_select: specify |
name: value |
intersect-A2.bed intersect-B2.bed value |
| Test-20 |
inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed overlap_mode: -wa split: False |
name: value |
intersectBed1.bed intersectBed2.bed value |
| Test-21 |
inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed overlap_mode: ['-wa', '-wb'] split: False |
name: value |
intersectBed1.bed intersectBed2.bed value |
| Test-22 |
inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed split: False invert: True |
name: value |
intersectBed1.bed intersectBed2.bed value |