| 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 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0 (this tool) |
| 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 |
| 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 |