| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.15.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.9.0 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.4 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.3.2 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.3.1 |
| toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.2 |
| spades |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| spades | 3.15.3 | package |
| zip | 3.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz value |
| Test-2 |
singlePaired|input1: ecoli_1K_1.fastq.gz singlePaired|input2: ecoli_1K_2.fastq.gz singlePaired|sPaired: paired mode_sel: ['--isolate', '--disable-rr', '--iontorrent'] cov_cond|cov_cutoff: auto kmer_cond|manual: 33 kmer_cond|kmer_sel: manual phred_offset: 33 optional_output: ['ag', 'ags', 'cn', 'cp', 'cs', 'sc', 'sp', 'ss', 'l'] |
name: value name: value name: value name: value name: value name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-3 |
operation_mode: --only-assembler singlePaired|input1: ecoli_1K_1.fastq.gz singlePaired|input2: ecoli_1K_2.fastq.gz singlePaired|sPaired: paired |
name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-4 |
singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: single additional_reads|singlePaired|input1: ecoli_1K_1.fastq.gz additional_reads|singlePaired|input2: ecoli_1K_2.fastq.gz additional_reads|singlePaired|sPaired: paired additional_reads|selector: true mode_sel: --careful |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-5 |
operation_mode: --only-assembler singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: single additional_reads|singlePaired|input1: ecoli_1K_1.fastq.gz additional_reads|singlePaired|input2: ecoli_1K_2.fastq.gz additional_reads|singlePaired|sPaired: paired additional_reads|selector: true mode_sel: --careful |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-6 |
operation_mode: --only-error-correction singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced mode_sel: --careful optional_output: ['cr', 'l'] |
name: value |
ecoli_1K.fastq.gz value |
| Test-7 |
operation_mode: --only-error-correction singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced mode_sel: ['--careful', '--sc'] optional_output: ['cr', 'l'] |
name: value |
ecoli_1K.fastq.gz value |
| Test-8 |
operation_mode: --only-assembler singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced mode_sel: --sc |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz value |
| Test-9 |
operation_mode: --only-error-correction singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced optional_output: ['cr', 'l'] |
name: value |
ecoli_1K.fastq.gz value |
| Test-10 |
operation_mode: --only-error-correction singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced mode_sel: --sc optional_output: ['cr', 'l'] |
name: value |
ecoli_1K.fastq.gz value |
| Test-11 |
singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced mode_sel: --sc |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz value |
| Test-12 |
singlePaired|input1: ecoli_1K_1.fastq.gz singlePaired|input2: ecoli_1K_2.fastq.gz singlePaired|sPaired: paired mode_sel: ['--sc', '--careful'] |
name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-13 |
operation_mode: --only-assembler singlePaired|input1: ecoli_1K_1.fastq.gz singlePaired|input2: ecoli_1K_2.fastq.gz singlePaired|sPaired: paired mode_sel: ['--sc', '--careful'] |
name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-14 |
singlePaired|input1: ecoli_1K.fastq.gz singlePaired|sPaired: paired_interlaced arf|nanopore: ecoli_1K.fastq.gz arf|pacbio: ecoli_1K.fastq.gz arf|sanger: ecoli_1K.fastq.gz arf|trusted_contigs: ecoli_1K.fasta.gz |
name: value name: value name: value name: value |
ecoli_1K.fastq.gz ecoli_1K.fasta.gz value |
| Test-15 |
singlePaired|input1: ecoli_1K_1.fastq.gz singlePaired|input2: ecoli_1K_2.fastq.gz singlePaired|type_paired: hqmp singlePaired|orientation: rf singlePaired|sPaired: paired |
name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |
| Test-16 |
singlePaired|input: list:paired collection singlePaired|type_paired: hqmp singlePaired|sPaired: paired_collection |
name: value name: value name: value name: value |
ecoli_1K_1.fastq.gz ecoli_1K_2.fastq.gz value |