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Stacks: assemble read pairs by locus tool metadata

Miscellaneous

Name: Stacks: assemble read pairs by locus

Description: run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers

Id: stacks_assembleperead

Guid: toolshed.g2.bx.psu.edu/repos/iuc/stacks_assembleperead/stacks_assembleperead/1.46.0

Version: 1.46.0

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/iuc/stacks_assembleperead/stacks_assembleperead/1.46.1

toolshed.g2.bx.psu.edu/repos/iuc/stacks_assembleperead/stacks_assembleperead/1.46.0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/stacks_assembleperead/stacks_assembleperead/1.42.0

toolshed.g2.bx.psu.edu/repos/iuc/stacks_assembleperead/stacks_assembleperead/1.40.1

toolshed.g2.bx.psu.edu/repos/iuc/stacks_assembleperead/stacks_assembleperead/1.40.0

stacks_assembleperead

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

Requirements:

name

version

type

stacks

1.46

package

velvet

1.2.10

package

stacks_summary

1.1

package

Functional tests

name

inputs

outputs

required files

Test-1

stacks_col: list collection
reads: ['demultiplexed/PopA_01.2.fq', 'demultiplexed/PopA_02.2.fq']

genotypes/batch_1.catalog.alleles.tsv
genotypes/batch_1.catalog.snps.tsv
genotypes/batch_1.catalog.tags.tsv
genotypes/PopA_01.alleles.tsv
genotypes/PopA_01.matches.tsv
genotypes/PopA_01.snps.tsv
genotypes/PopA_01.tags.tsv
genotypes/PopA_02.alleles.tsv
genotypes/PopA_02.matches.tsv
genotypes/PopA_02.snps.tsv
genotypes/PopA_02.tags.tsv
demultiplexed/PopA_01.2.fq
demultiplexed/PopA_02.2.fq

Test-2

velvet|contig_length: 20
stacks_col: list collection
reads: ['demultiplexed/PopA_01.2.fq', 'demultiplexed/PopA_02.2.fq']
velvet|use_velvet: yes

attributes: name