| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.29.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.19.1 |
| bedtools_coveragebed |
| 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 |
bedtools coverage
$d
$hist
$split
$strandedness
$mean
#if str($overlap_a):
-f $overlap_a
#end if
#if str($overlap_b):
-F $overlap_b
#end if
$reciprocal_overlap
$a_or_b
-a '$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
#end if
$sorted
#if str($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 $inputA.is_of_type('gff'):
| sort -k1,1 -k4,2n
#else:
| sort -k1,1 -k2,2n
#end if
> '$output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputA: coverageBedA.bed reduce_or_iterate|inputB: coverageBedB.bed |
name: value |
coverageBedA.bed coverageBedB.bed value |
| Test-2 |
inputA: multiCov1.bed reduce_or_iterate|inputB: srma_in3.bam sorted: True |
name: value |
multiCov1.bed srma_in3.bam value |
| Test-3 |
inputA: multiCov1.bed reduce_or_iterate|inputB: srma_in3.bam reduce_or_iterate|reduce_or_iterate_selector: reduce sorted: True |
name: value |
multiCov1.bed srma_in3.bam value |
| Test-4 |
inputA: coverageBedA.bed reduce_or_iterate|inputB: coverageBedB.bed overlap_b: 1 |
name: value |
coverageBedA.bed coverageBedB.bed value |
| Test-5 |
inputA: coverageBedA.bed reduce_or_iterate|inputB: coverageBedB.bed overlap_a: 1E-5 reciprocal_overlap: True |
name: value |
coverageBedA.bed coverageBedB.bed value |
| Test-6 |
inputA: multiCov1.bed reduce_or_iterate|inputB: ['srma_in3.bam', 'coverageBed.bam'] reduce_or_iterate|reduce_or_iterate_selector: reduce sorted: True |
name: value |
multiCov1.bed srma_in3.bam coverageBed.bam value |
| Test-7 |
inputA: coverageBedA2.bed reduce_or_iterate|inputB: coverageBed.bam |
name: value |
coverageBedA2.bed coverageBed.bam value |
| Test-8 |
inputA: coverageBedA2.bed reduce_or_iterate|inputB: coverageBed.bam mean: True |
name: value |
coverageBedA2.bed coverageBed.bam value |