Repository revision
27:9a776b080193

Repository 'sra_tools'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sra_tools

Download and Extract Reads in FASTQ tool metadata
Miscellaneous
format from NCBI SRA
fastq_dump
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.0+galaxy0
3.0.0+galaxy0
fastq-dump --version | tr -d $'\n'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/3.0.0+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/1.2.5
fastq_dump
Requirements (dependencies defined in the <requirements> tag set)
name version type
sra-tools 3.0.0 package
pigz 2.6 package
samtools 1.16.1 package
Functional tests
name inputs outputs required files
Test-1 input|accession: SRR044777
input|input_select: accession_number
outputformat: fastqsanger
adv|skip_technical: True
Test-2 input|accession: SRR925743
input|input_select: accession_number
outputformat: fastqsanger.gz
adv|maxID: 5
Test-3 input|accession: SRR925743
input|input_select: accession_number
outputformat: fastqsanger
adv|maxID: 5
Test-4 input|file_list: list_pe
input|input_select: file_list
outputformat: fastqsanger
adv|maxID: 5
list_pe
Test-5 input|file_list: list_pe2
input|input_select: file_list
outputformat: fastqsanger
adv|maxID: 5
list_pe2
Test-6 input|file_list: list_se
input|input_select: file_list
outputformat: fastqsanger
adv|maxID: 5
list_se
Test-7 input|accession: SRR6982805
input|input_select: accession_number
outputformat: fastqsanger.gz
adv|maxID: 2
adv|table: SEQUENCE
Test-8 input|accession: ERR086330, SRR11953971
input|input_select: accession_number
outputformat: fastqsanger.gz