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Repository revision

Revision: 6:dc6ff68ea5e8

Repository 'samtool_filter2'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2

Filter SAM or BAM, output SAM or BAM tool metadata

Miscellaneous

Name: Filter SAM or BAM, output SAM or BAM

Description: files on FLAG MAPQ RG LN or by region

Id: samtool_filter2

Guid: toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2

Version: 1.1.2

Version command string: None

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8

toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2 (this tool)

toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.1

samtool_filter2

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

header:
flag|reqBits: 0x0080
input1: bam_to_sam_in2.sam
outputtype: sam
flag|filter: yes

output1: None

bam_to_sam_in2.sam

Test-2

header:
read_group: rg1
input1: bam_to_sam_in2.sam
outputtype: sam
flag|filter: no

output1: None

bam_to_sam_in2.sam

Test-3

input1: bam_to_sam_in1.sam
flag|filter: yes
outputtype: sam
header:
flag|skipBits: 0x0008
mapq: 250

output1: None

bam_to_sam_in1.sam