Repository revision
2:b8827c571fbd

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

Stacks: de novo map tool metadata
Miscellaneous
the Stacks pipeline without a reference genome (denovo_map.pl)
stacks_denovomap
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.40.0
1.40.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.40.1
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.40.0 (this tool)
stacks_denovomap
Requirements (dependencies defined in the <requirements> tag set)
name version type
stacks 1.40 package
velvet 1.2.10 package
Functional tests
name inputs outputs required files
Test-1 options_usage|rad_analysis_type: genetic
options_usage|parent_sequences: demultiplexed/PopA_01.1.fq
options_usage|progeny_sequences: demultiplexed/PopA_02.1.fq
output_log: None
catalogtags: None
catalogsnps: None
catalogalleles: None
out_generic_haplo: None
out_sql_markers: None
out_joinmap: None
out_sql_genotypes: None
demultiplexed/PopA_01.1.fq
demultiplexed/PopA_02.1.fq
Test-2 options_usage|individual_sample: ['demultiplexed/PopA_01.1.fq', 'demultiplexed/PopA_02.1.fq', 'demultiplexed/PopA_03.1.fq', 'demultiplexed/PopA_04.1.fq', 'demultiplexed/PopB_01.1.fq', 'demultiplexed/PopB_02.1.fq', 'demultiplexed/PopB_03.1.fq', 'demultiplexed/PopB_04.1.fq']
options_usage|rad_analysis_type: population
options_usage|popmap: denovo_map/popmap.tsv
output_log: None
catalogtags: None
catalogsnps: None
catalogalleles: None
out_haplotypes: None
out_hapstats: None
out_populations_log: None
out_sumstats_sum: None
out_sumstats: None
demultiplexed/PopA_01.1.fq
demultiplexed/PopA_02.1.fq
demultiplexed/PopA_03.1.fq
demultiplexed/PopA_04.1.fq
demultiplexed/PopB_01.1.fq
demultiplexed/PopB_02.1.fq
demultiplexed/PopB_03.1.fq
demultiplexed/PopB_04.1.fq
denovo_map/popmap.tsv