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Repository revision

Revision: 2:167765a633c0

Repository 'count_roi_variants'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants

Count sequence variants in region of interest tool metadata

Miscellaneous

Name: Count sequence variants in region of interest

Description: using samtools view

Id: count_roi_variants

Guid: toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants/count_roi_variants/0.0.6

Version: 0.0.6

Version command string: python $__tool_directory__/count_roi_variants.py --version

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants/count_roi_variants/0.0.6 (this tool)

toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants/count_roi_variants/0.0.5

toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants/count_roi_variants/0.0.3

count_roi_variants

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

samtools

1.2

package

Functional tests

name

inputs

outputs

required files

Test-1

input_bam: ex1.bam
region: chr2:400-406

name: value

ex1.bam
value

Test-2

input_bam: coverage_test.bam
region: ref:10-15

name: value

coverage_test.bam
value

Test-3

input_bam: SRR639755_mito_pairs_vs_NC_010642_clc.bam
region: gi|187250362|ref|NC_010642.1|:1695-1725

name: value

SRR639755_mito_pairs_vs_NC_010642_clc.bam
value

Test-4

input_bam: SRR639755_mito_pairs_vs_NC_010642_clc.bam
region: ref:1695-1725

SRR639755_mito_pairs_vs_NC_010642_clc.bam