| 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 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.2 (this tool) |
| 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 | 2.29.2 | package |
| samtools | 1.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-2 |
inputA: intersect-query.bed reduce_or_iterate|reduce_or_iterate_selector: reduce reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] |
attributes: name |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed name |
| Test-3 |
overlap_mode: ['-wa', '-wb'] inputA: intersect-query.bed reduce_or_iterate|reduce_or_iterate_selector: reduce reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] sorted: True |
attributes: name |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed name |
| Test-4 |
reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] overlap_mode: ['-wa', '-wb'] inputA: intersect-query.bed reduce_or_iterate|names: True sorted: True reduce_or_iterate|reduce_or_iterate_selector: reduce |
attributes: name |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed name |
| Test-5 |
sorted: True invert: True inputA: intersect-query.bed reduce_or_iterate|reduce_or_iterate_selector: reduce reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] |
attributes: name |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed name |
| Test-6 |
reduce_or_iterate|inputB: ['intersect-d1.bed', 'intersect-d2.bed', 'intersect-d3.bed'] overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 1.0 inputA: intersect-query.bed fraction_cond|fraction_select: specify sorted: True reduce_or_iterate|reduce_or_iterate_selector: reduce |
attributes: name |
intersect-query.bed intersect-d1.bed intersect-d2.bed intersect-d3.bed name |
| Test-7 |
overlap_mode: -wa inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-8 |
overlap_mode: -wb inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-9 |
overlap_mode: ['-wa', '-wb'] inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-10 |
overlap_mode: -loj inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-11 |
overlap_mode: -wo inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-12 |
overlap_mode: -wao inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-13 |
inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed once: True |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-14 |
count: True inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-15 |
invert: True inputA: intersect-A.bed reduce_or_iterate|reduce_or_iterate_selector: iterate reduce_or_iterate|inputB: intersect-B.bed |
attributes: name |
intersect-A.bed intersect-B.bed name |
| Test-16 |
reduce_or_iterate|inputB: intersect-B2.bed overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 inputA: intersect-A2.bed fraction_cond|fraction_select: specify reduce_or_iterate|reduce_or_iterate_selector: iterate |
attributes: name |
intersect-A2.bed intersect-B2.bed name |
| Test-17 |
reduce_or_iterate|inputB: intersect-B2.bed fraction_cond|fraction_select: specify fraction_cond|overlap: 0.5 inputA: intersect-A2.bed overlap_mode: ['-wa', '-wb'] reduce_or_iterate|reduce_or_iterate_selector: iterate fraction_cond|reciprocal_cond|reciprocal: -r |
attributes: name |
intersect-A2.bed intersect-B2.bed name |
| Test-18 |
reduce_or_iterate|inputB: intersect-B2.bed overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|reciprocal_cond|overlapB: 0.5 inputA: intersect-A2.bed fraction_cond|fraction_select: specify reduce_or_iterate|reduce_or_iterate_selector: iterate |
attributes: name |
intersect-A2.bed intersect-B2.bed name |
| Test-19 |
reduce_or_iterate|inputB: intersect-B2.bed fraction_cond|reciprocal_cond|disjoint: True overlap_mode: ['-wa', '-wb'] fraction_cond|overlap: 0.5 fraction_cond|reciprocal_cond|overlapB: 0.5 inputA: intersect-A2.bed fraction_cond|fraction_select: specify reduce_or_iterate|reduce_or_iterate_selector: iterate |
attributes: name |
intersect-A2.bed intersect-B2.bed name |
| Test-20 |
overlap_mode: -wa inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed split: False |
attributes: name |
intersectBed1.bed intersectBed2.bed name |
| Test-21 |
overlap_mode: ['-wa', '-wb'] inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed split: False |
attributes: name |
intersectBed1.bed intersectBed2.bed name |
| Test-22 |
invert: True inputA: intersectBed1.bed reduce_or_iterate|inputB: intersectBed2.bed split: False |
attributes: name |
intersectBed1.bed intersectBed2.bed name |