Repository revision
5:6aad515a5270

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

plasmidSPAdes tool metadata
Miscellaneous
extract and assembly plasmids from WGS data
spades_plasmidspades
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.4+galaxy1
3.15.4+galaxy1
spades.py --version 2>&1 | awk -F 'v' '{print $2}'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.4+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.4+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.3+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/spades_plasmidspades/spades_plasmidspades/3.15.3+galaxy0
spades_plasmidspades
Requirements (dependencies defined in the <requirements> tag set)
name version type
spades 3.15.4 package
zip 3.0 package
Functional tests
name inputs outputs required files
Test-1 singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
name: value
name: value
name: value
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-2 singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
phred_offset: 33
optional_output: ['ag', 'ags', 'cn', 'cp', 'cr', 'cs', 'l', 'sc', 'sp', 'ss']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
name: value
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-3 operation_mode: --only-assembler
additional_reads|singlePaired|input1: pl1.fq.gz
additional_reads|singlePaired|input2: pl2.fq.gz
additional_reads|singlePaired|sPaired: paired
additional_reads|selector: true
mode_sel: --careful
optional_output: l
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-4 singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
mode_sel: --careful
optional_output: l
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-5 operation_mode: --only-error-correction
singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
optional_output: ['cr', 'l']
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-6 operation_mode: --only-error-correction
singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
optional_output: ['cr', 'l']
name: value
pl1.fq.gz
pl2.fq.gz
value
Test-7 singlePaired|input1: pl1.fq.gz
singlePaired|input2: pl2.fq.gz
singlePaired|sPaired: paired
arf|nanopore: ecoli_1K.fastq.gz
arf|pacbio: ecoli_1K.fastq.gz
arf|sanger: ecoli_1K.fastq.gz
arf|untrusted_contigs: ecoli_1K.fasta.gz
mode_sel: --careful
optional_output: ['cr', 'l']
name: value
pl1.fq.gz
pl2.fq.gz
ecoli_1K.fastq.gz
ecoli_1K.fasta.gz
value