Galaxy |

Repository revision

Revision: 28:4df8de2d0e48

Repository 'sra_tools'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sra_tools

Download and Extract Reads in BAM tool metadata

Miscellaneous

Name: Download and Extract Reads in BAM

Description: format from NCBI SRA

Id: sam_dump

Guid: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.0.3+galaxy0

Version: 3.0.3+galaxy0

Version command string: sam-dump --version | tr -d $'\n'

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.0.5+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.0.3+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/3.0.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.11.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.8+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/1.2.5

sam_dump

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

Requirements:

name

version

type

sra-tools

3.0.3

package

pigz

2.6

package

samtools

1.16.1

package

Functional tests

name

inputs

outputs

required files

Test-1

input|accession: SRR925743
input|input_select: accession_number
outputformat: sam
adv|region: 17:41243452-41277500

Test-2

input|accession: SRR925743,SRR522874
input|input_select: accession_number
outputformat: sam
adv|region: 17:41243452-41277500